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EPA 620/R-04/200 
February 2005 


Condition of Estuaries of the Western United 
States for 1999: A Statistical Summary 



Office of Research and Development 
U.S. Environmental Protection Agency 
Washington, DC 20460 


List of Authors 


Walter G. Nelson 1 , Henry Lee II 1 , Janet O. Lamberson 1 , Virginia Engle 2 , Linda Harwell 2 , 

Lisa M. Smith 2 


List of Author Affiliations 

1 Western Ecology Division, National Health and Environmental Effects Research 
Laboratory, U.S. Environmental Protection Agency, Newport OR 97365 

2 Gulf Ecology Division, National Health and Environmental Effects Research 
Laboratory, U.S. Environmental Protection Agency, Gulf Breeze FL 32561 


n 


Preface 


This document is the statistical summary for the western states, coastal component of 
the nationwide Environmental Monitoring and Assessment Program (EMAP). The focus 
of the study during 1999 was the small estuaries of Washington, Oregon, and California 
(excluding Puget Sound, the main channel of the Columbia River, and San Francisco 
Bay). EMAP-West is a partnership of the States of California, Oregon and Washington, 
the National Oceanic and Atmospheric Administration (NOAA), and the U.S. 
Environmental Protection Agency (EPA). The program is administered through the EPA 
and implemented through partnerships with a combination of federal and state 
agencies, universities and the private sector. 

The appropriate citation for this report is: 

Nelson, Walter G., Lee II, Henry, Lamberson, Janet O., Engle, Virginia, Harwell, 
Linda, Smith, Lisa M. 2004. Condition of Estuaries of Western United States for 
1999: A Statistical Summary. Office of Research and Development, National 
Health and Environmental Effects Research Laboratory, EPA/620/R-04/200. 


Disclaimer 

The information in this document has been funded wholly or in part by the U.S. 
Environmental Protection Agency under Cooperative Agreements with the states of 
Washington (CR 827869 ), Oregon (CR 87840 ), and California (CR 827870 ) and an 
Inter Agency Agreement with the National Marine Fisheries Service (DW 13938780). It 
has been subjected to review by the National Health and Environmental Effects 
Research Laboratory and approved for publication. Approval does not signify that he 
contents reflect the views of the agency, nor does mention of trade names or 
commercial products constitute endorsement or recommendation for use. 


Acknowledgments 


Western Coastal EMAP involves the cooperation of a significant number of federal, 
state, and local agencies. The project has been principally funded by the U.S. 
Environmental Protection Agency Office of Research and Development. The following 
organizations provided a wide range of field sampling, analytical and interpretive 
support in their respective states through individual cooperative agreements with EPA: 
Washington Department of Ecology, Oregon Department of Environmental Quality, 
Southern California Coastal Water Research Project (SCCWRP). The Northwest 
Fisheries Science Center, National Marine Fisheries Service, National Oceanic and 
Atmospheric Administration provided field support and analysis offish pathologies 
through a cooperative agreement with EPA. Other research organizations provided 
additional scientific support through subcontracts with these lead organizations. Moss 
Landing Marine Laboratory provided the field crews for collection of samples in 
California under contract to SCCWRP. 

The U.S. Geological Survey, Columbia Environmental Research Center, through the 
Biomonitoring Environmental Status and Trends (BEST) Program, provided analyses for 
H4IIE bioassay-derived 2,3,7,8-tetrachlorodibenzo - p -dioxin equivalents (TCDD-EQ) 
for exposure offish to planar halogenated hydrocarbons. Through their Marine 
Ecotoxicology Research Station, BEST also provided two bioassays on sediment 
porewater toxicity, the sea urchin Arbacia punctulata fertilization toxicity and embryo 
development toxicity tests. 

Project wide information management support was provided by SCCWRP as part of 
their cooperative agreement. 

Many individuals within EPA made important contributions to Western Coastal EMAP. 
Critical guidance and vision in establishing this program was provided by Kevin 
Summers of Gulf Ecology Division. Tony Olsen of Western Ecology Division (WED) has 
made numerous comments which have helped to improve the quality of this document. 
Lorraine Edmond of the Region 10 Office of EPA and Terrence Fleming of the Region 9 
Office of EPA have ably served as the regional liaisons with the state participants in 
their regions. Robert Ozretich of WED performed a detailed review of the database 
contents used for this analysis, and we additionally thank him for his extensive quality 
assurance review of this document. 

We thank Jeff Hyland of NOAA and Joan Cabreza of the Region 10 Office of EPA for 
their technical reviews of this report. 

The success of the Western Coastal pilot has depended on the contributions and 
dedication of many individuals. Special recognition for their efforts is due the following 
participants: 


IV 


Washington Department of Ecology 
Casey Cliche 
Margaret Dutch 
Ken Dzinbal 
Christina Ricci 
Kathy Welch 


Oregon Department of Environmental Quality 

Mark Bautista 
Greg Coffeen 
Curtis Cude 
Paula D’Alfonso 
RaeAnn Haynes 
Dan Hickman 
Bob McCoy 
Greg McMurray 
Greg Pettit 
Chris Redmond 
Crystal Sigmon 
Daniel Sigmon 
Scott Sloane 

Southern California Coastal Water Research Project (SCCWRP) 

Larry Cooper 
Steve Weisberg 

Moss Landing Marine Laboratory 

Russell Fairey 
Cassandra Roberts 

San Francisco Estuary Institute 

Bruce Thompson 

University of California Davis 

Brian Anderson 

National Oceanic and Atmospheric Administration 

National Marine Fisheries Service, Northwest Fisheries Science Center 
Bernie Anulacion 
Tracy Collier 
Dan Lomax 
Mark Myers 
Paul Olson 


v 










U.S. Geological Survey 

Biomonitoring of Environmental Status and Trends Program (BEST) 
Christine Bunck 

Columbia Environmental Research Center 
Don Tillet 

Marine Ecotoxicology Research Station 
Scott Carr 

Gulf Breeze Project Office 
Tom Heitmuller 
Steve Robb 
Pete Bourgeois 

U.S. Environmental Protection Agency 

Office of Research and Development 
Tony Olsen 
Steve Hale 
John Macauley 

Region 9 

Terrence Fleming 
Janet Hashimoto 

Region 10 

Lorraine Edmond 
Gretchen Hayslip 

Indus Corporation 

Patrick Clinton 


VI 





Table of Contents 


Preface .iii 

Disclaimer .iii 

Acknowledgments .iv 

List of Figures . x 

List of Tables .xiv 

Executive Summary .xvi 

1.0 Introduction . 1 

1.1 Program Background . 1 

1.2 The Western United States Context for 

a Coastal Condition Assessment . 2 

1.3 Objectives . 3 

2.0 Methods . 5 

2.1 Sampling Design and Statistical Analysis Methods . 5 

2.1.1 Background . 5 

2.1.2 Sampling Design . 6 

2.1.2.1 1999 West Coast Design . 6 

2.1.2.2 2000 West Coast Design . 8 

2.2 Data Analysis . 21 

2.3 Indicators . 24 

2.3.1 Water Measurements . 27 

2.3.1.1 Hydrographic Profile . 27 

2.3.1.2 Water Quality Indicators . 28 


VII 

























2.3.2 Sediment Toxicity Testing . 29 

2.3.2.1 Sediment Collection . 29 

2.3.2.2 Laboratory Test Methods . 30 

2.3.2.2.1 Amphipod Toxicity Tests . 30 

2.3.2.2.2 Sea Urchin Toxicity Tests . 31 

2.3.3 Biotic Condition Indicators . 32 

2.3.3.1 Benthic Community Structure . 32 

2.3.3.2 Fish Trawls . 33 

2.3.3.3 Fish Community Structure . 34 

2.3.3.4 Fish Contaminant Sampling . 34 

2.3.3.5 Fish Contaminant Chemistry Analyses . 35 

2.3.3.6 Fish Gross Pathology . 36 

2.3.4 Sediment Chemistry . 36 

2.4 General QA/QC Process . 41 

2.4.1 QA of Chemical Analyses . 42 

2.4.2 QA of Taxonomy. 50 

2.5 Data Management . 52 

2.6 Unsamplable Area . 52 

3.0 Indicator Results . 55 

3.1 Habitat Indicators . 55 

3.1.1 Salinity . 55 

3.1.2 Water Temperature . 55 

3.1.3 pH . 55 

viii 

























3.1.4 Sediment Characteristics 


56 


3.1.5 Water Quality Parameters . 56 

3.1.6 Water Column Stratification . 57 

3.2 Exposure Indicators . 73 

3.2.1 Dissolved Oxygen . 73 

3.2.2 Sediment Contaminants . 73 

3.2.2.1 Sediment Metals . 73 

3.2.2.2 Sediment Organics . 91 

3.2.3 Sediment Toxicity . 99 

3.2.3.1 Ampelisca abdita . 99 

3.2.3.2 Arbacia punctulata . 99 

3.2.4 Tissue Contaminants . 108 

3.3 Biotic Condition Indicators . 115 

3.3.1 Infaunal Species Richness and Diversity . 115 

3.3.2 Infaunal Abundance and Taxonomic Composition . 116 

3.3.3 Demersal Species Richness and Abundance . 124 


4.0 References 


129 


























List of Figures 


Figure 2-1. Location of Washington EMAP survey sites. 10 

Figure 2-2. Location of EMAP survey sites along the northern portion 

of the Oregon coast, including survey sites for the intensification study of 
Tillamook Bay. 11 

Figure 2-3. Location of EMAP survey sites along the southern portion 

of the Oregon coast. 12 

Figure 2-4. Location of EMAP survey sites for the intensification study 

of Tillamook Bay, Oregon. 13 

Figure 2-5. Location of California EMAP survey sites in Northern California 

from the Oregon Border to the Garcia River. 14 

Figure 2-6. Location of California EMAP survey sites in Northern and 

Central California from the Russian River to the Santa Ynez River.15 

Figure 2-7. Location of California EMAP survey sites in Central and 

Southern California from Santa Barbara to the Mexican border. 16 

Figure 3.1-1. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. salinity of bottom waters.58 

Figure 3.1-2. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. temperature of bottom waters. 59 

Figure 3.1-3. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. pH in bottom waters.60 

Figure 3.1-4. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. percent silt-clay of sediments.61 

Figure 3.1-5. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. percent total organic carbon of sediments.62 

Figure 3.1-6. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. water column mean concentration of chlorophyll a. . . 63 

Figure 3.1-7. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. water column mean nitrate + nitrite concentration. ... 64 


x 














Figure 3.1-8. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. water column mean ammonium concentration.65 

Figure 3.1-9. Percent area (and 95% C.l.) of small estuaries of the 
West Coast states vs. water column mean total nitrogen 

(nitrate + nitrite + ammonium) concentration.66 


Figure 3.1-10. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. water column mean orthophosphate concentration. . . 67 

Figure 3.1-11. Percent area (and 95% C.l.) of small estuaries of the 
West Coast states vs. water column mean ratio of total nitrogen 
(nitrate + nitrite + ammonium) concentration to total orthophosphate 
concentration. 68 

Figure 3.1-12. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. water column total suspended solids concentration. . 69 


Figure 3.1-13. Percent area (and 95% C.l.) of small estuaries of the 
West Coast states vs. percent light transmission estimated 
at a reference depth of 1 m in the water column.70 

Figure 3.1-14. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. water column stratification index.71 

Figure 3.1-15. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. Ao t stratification index. 72 

Figure 3.2-1. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. dissolved oxygen of bottom waters.74 

Figure 3.2-2. Percent area (and 95% C.l.) of small estuaries of the 

West Coast states vs. dissolved oxygen of surface waters.75 

Figure 3.2-3. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of arsenic.80 

Figure 3.2-4. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of cadmium. 81 

Figure 3.2-5. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of chromium. 82 


XI 














Figure 3.2-6. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of copper. 83 

Figure 3.2-7. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of lead. 84 

Figure 3.2-8. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of mercury. 85 

Figure 3.2-9. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of nickel. 86 

Figure 3.2-10. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of selenium.87 

Figure 3.2-11. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of silver. 88 

Figure 3.2-12. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of tin. 89 

Figure 3.2-13. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of zinc. 90 

Figure 3.2-14. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of total PAHs. 94 

Figure 3.2-15. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of high molecular weight PAHs. 95 

Figure 3.2-16. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of low molecular weight PAHs. 96 

Figure 3.2-17. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of total PCBs. 97 

Figure 3.2-18. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. sediment concentration of total DDT. 98 

Figure 3.2-19. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. percent control corrected survivorship of Ampelisca abdita . 101 


XII 
















Figure 3.2-20. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
fertilization of Arbacia punctulata eggs for the 100% water quality adjusted 
porewater concentration. 102 

Figure 3.2-21. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
fertilization of Arbacia punctulata eggs for the 50% water quality adjusted 
porewater concentration. 103 

Figure 3.2-22. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
fertilization of Arbacia punctulata eggs for the 25% water quality adjusted 
porewater concentration. 104 

Figure 3.2-23. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
successful embryonic development of Arbacia punctulata for the 100% water 
quality adjusted porewater concentration. 105 

Figure 3.2-24. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
successful embryonic development of Arbacia punctulata for the 50% water 
quality adjusted porewater concentration. 106 

Figure 3.2-25. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
successful embryonic development of Arbacia punctulata for the 25% water 
quality adjusted porewater concentration. 107 

Figure 3.3-1. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. benthic infaunal species richness. 118 

Figure 3.3-2. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. benthic infaunal FI' diversity. 119 

Figure 3.3-3. Percent area (and 95% C.l.) of West Coast small estuaries 

vs. benthic infaunal total abundance. 120 


XIII 












List of Tables 


Table 2-1. West Coast sampling sites with station coordinates of locations sampled. 17 

Table 2-2. Core environmental indicators for the EMAP Western Coastal survey. . . 25 

Table 2-3. Environmental indicators under development or conducted 

by collaborators during the EMAP Western Coastal survey.26 

Table 2-4. Compounds analyzed in all three states in sediments and fish tissues. . . 37 

Table 2-5. Summary of EMAP-Coastal chemistry sample collection, 

preservation, and holding time requirements for sediment and fish tissues. . 38 

Table 2-6. Methods used to analyze for contaminants in sediments and tissues. . . 39 

Table 2-7. Units, method detection limits (MDL), and reporting limits (RL) 

for sediment chemistry. 44 

Table 2-8. Units, method detection limits (MDL), and reporting limits (RL) 

for tissue chemistry for compounds measured in all three states.46 

Table 2-9. Summary of reference and matrix spike recoveries, and relative percent 

differences (RPD) of duplicates. 48 

Table 2-10. Listing of primary and QA/QC taxonomists by taxon and region 

for the 1999 Western Coastal EMAP study. 51 

Table 3.2-1. Summary statistics for sediment metal concentrations (pg/g) 

for 190 stations from West Coast estuaries. 79 

Table 3.2-2. Mean sediment concentrations (ng/g dry weight) and frequency of 

detection of the PAHs, PCBs and pesticides measured in all three states. . 93 

Table 3.2-3. Species composition and relative abundance of the three 

fish groups used in the tissue residue analysis. 110 

Table 3.2-4. Fish tissue residues of metals measured in all three states.Ill 

Table 3.2-5. Fish tissue residues of total PCBs, total DDT and the 

additional pesticides measured in all three states. 113 

Table 3.3-1. Summary statistics for benthic abundance, number of 

species per benthic sample, and H'. 121 


XIV 












Table 3.3-2. Abundance, taxonomic grouping, and classification of the 

ten most abundant benthic species in the three states including the 
intensification sites in Northern California and Tillamook, Oregon.122 

Table 3.3-3. Abundance, taxonomic grouping, and classification of the 
ten most abundant benthic species in the three states excluding 
the Northern California intensification stations. 123 

Table 3.3-4. Trawl duration and speed averaged across California, Oregon, 

and Washington and in each individual state. 125 

Table 3.3-5. Mean number of fish captured per trawl and mean number 
offish species per trawl averaged across California, Oregon, and 
Washington and for each individual state. 126 

Table 3.3-6. Ten numerically dominant fish species averaged across California, 

Oregon, and Washington, including both the base and intensive stations. . 127 

Table 3.3-7 Mean and standard deviation of the five most numerically abundant fish 

species in California, Oregon, and Washington. 128 


xv 










Executive Summary 

As a part of the National Coastal Assessment, the Environmental Monitoring and 
Assessment Program (EMAP) initiated a five-year Western Coastal component in 1999. 
The objectives of the program were: to assess the condition of estuarine resources of 
Washington, Oregon and California based on a range of indicators of environmental 
quality using an integrated survey design; to establish a baseline for evaluating how the 
conditions of the estuarine resources of these states change with time; to develop and 
validate improved methods for use in future coastal monitoring and assessment efforts 
in the western coastal states; and to transfer the technical approaches and methods for 
designing, conducting and analyzing data from probability based environmental 
assessments to the states and tribes. 

The focus of the study during 1999 was the small estuaries of Washington, Oregon, and 
California, excluding Puget Sound, the main channel of the Columbia River, and San 
Francisco Bay, which were sampled in 2000 during the second year of the program. 

The environmental condition indicators used in this study included measures of: 1) 
general habitat condition (depth, salinity, temperature, pH, total suspended solids, 
sediment characteristics), 2) water quality indicators (chlorophyll a, nutrients), 3) 
pollutant exposure indicators (dissolved oxygen concentration, sediment contaminants, 
fish tissue contaminants, sediment toxicity), and 4) benthic condition indicators (diversity 
and abundance of benthic infaunal and demersal fish species, fish pathological 
anomalies). 

The study utilized a stratified random sampling design, with the base study consisting of 
150 sites equally divided among the three states. Additionally, intensification studies 
were conducted that consisted of 30 sites located in Tillamook Bay, Oregon, and 30 
sites distributed among the mouths of river dominated estuaries in northern California. 

All sites were combined for statistical analysis. Cumulative distribution functions (CDFs) 
were produced using appropriate sampling area weightings to represent the areal extent 
associated with given values of an indicator variable for the small estuaries of the West 
Coast. 

Reflecting the fact that the sampling effort spanned both the Columbian and Californian 
Biogeographic Provinces, the indicators of general habitat condition showed wide 
ranges of values, e.g., bottom water temperatures from 8.5 to 32.1 °C. Approximately 
54% of the area of the small West Coast estuaries would be classified as euhaline (>30 
psu) based on the EMAP sampling. Approximately 65% of the estuarine area had 
sandy sediments (<20% silt clay), 29% had intermediate muddy sands (20-80% silt 
clay), and 6 % had mud sediments (>80% silt clay). The TOC content of sediments was 
< 1% in approximately 84% of the area of the small West Coast estuaries. 

The pH of bottom waters for the small estuaries of West Coast states had the 
surprisingly wide range of from 5.1 to 10.2, with extreme values associated with low 
salinity locations. There was no geographic pattern to high values of chlorophyll a. 


XVI 


Most water quality indicators showed similar CDF patterns, with high values being 
observed in a very small percentage of estuarine area, thus generating extensive right 
hand tails to CDF distributions. For example, the average water column concentration of 
nitrate/nitrite of small West Coast estuaries ranged from 0 to 3472 pg L' 1 , but only 2.7 % 
of estuarine area had nitrate/nitrite values that exceeded concentrations of 300 pgL' 1 . 
Approximately 75% of estuarine area had molar ratios of average water column total 
nitrogen to total phosphorus (N/P) values < 16, suggesting nitrogen limitation. While 
total suspended solids (TSS) ranged from 0 to 276.2 mg L' 1 , approximately 95% of 
estuarine area had TSS < 19.1 mg L' 1 . Only about 12 % of estuarine area showed an 
indication of strong water column stratification as indicated by the difference in surface 
and bottom salinities, suggesting the estuarine areas sampled are generally well mixed. 

Among pollution exposure indicators, less than four percent of estuarine area had 
dissolved oxygen concentrations in bottom waters below 5 mg/L. High values of 
potentially toxic metals generally occurred in a very small percentage of the estuarine 
area sampled, with maximum values of many of the metals being observed in the highly 
urbanized Los Angeles Harbor (cadmium, copper, lead, selenium, silver, tin, zinc). DDT 
and other pesticides were detected in a relatively small percentage of estuarine area. 
Seventy- three percent of estuarine area had non-detectable levels of total PCBs. 
Highest levels of organic contaminants (pesticides, PAHs) generally were associated 
with urbanized estuaries of southern California. 

Sediment toxicity tests with the amphipod Ampelisca abdita had control-corrected 
survivorship < 80 % in only about 9 % of estuarine area. Using sediment pore water 
bioassays, the control corrected, percent fertilization of eggs of the sea urchin Arbacia 
punctulata was < 91 % in only about 10.5 % of estuarine area for the 100% of the water 
quality adjusted (WQA) porewater treatment. Survivorship was higher for both 50% and 
25% WQA porewater treatments. For a similar test using percent successful 
development of Arbacia punctulata embryos, the control-corrected normal development 
of embryos was < 91 % in about 49 % of area of small West Coast estuaries for the 
100% of the WQA porewater treatment. Normal embryo development was higher for 
both 50% and 25% WQA porewater treatments. 

There was a total of 144 successful trawls across the three states, but due to the 
number of stations without successful trawls, the analysis of the fish trawl data is limited 
to summary statistics and species composition, and no CDFs are presented. The 
number of individuals per trawl averaged 33.7 fish per trawl, with a low of 13.9 in 
Oregon and a high of 68.0 in California. Species richness averaged 3.53 fish species 
per trawl, with a low of 2.63 in Oregon and a high of 5.46 in California. A report on the 
frequency offish pathologies will be produced separately by NOAA. 

Obtaining the target organisms (flatfish) for tissue analysis of contaminants proved 
difficult, and tissue analyses were conducted on only 53% of the total stations occupied. 
Thus cumulative distribution functions were not computed. There was no consistent 
spatial pattern in location of maximum fish tissue metal concentrations, with highest 


XVII 







values of mercury being recorded in several California estuaries, highest arsenic and 
lead values being recorded in several Washington estuaries, and highest copper values 
being recorded in an Oregon estuary. Maximum fish tissue residues for total PCBs 
were associated with urbanized estuaries in California, which were also associated with 
highest sediment concentrations of these contaminants. Tissue residues of DDT and its 
metabolites were considerably higher than other pesticides measured. 

A total of 187 samples of benthic infauna (>1 mm) were obtained using either grabs or a 
combination of smaller corers to obtain equivalent surface area (0.1 m 2 ). Reflecting the 
wide geographic distribution of sampling, a total of 841 non-colonial benthic taxa were 
recorded. Species richness ranged from 1 to 157 taxa per sample. Lowest species 
richness tended to be associated with low salinity sites, and highest species richness 
was associated with salinities > 30 psu. About 50% of the area of small West Coast 
estuaries had species richness < 17 species per sample. The northern California 
intensive study sites tended to have lower species richness and H' diversity values than 
other stations. 

Benthic infaunal abundance averaged 1378.9 individuals per sample, with lowest mean 
abundance per sample in Washington estuaries and highest mean abundance values in 
California estuaries, particularly the northern California intensive study sites. About 
50% of the area of small West Coast estuaries had mean infaunal abundance < 151 
individuals per sample. Two amphipod species (Americorophium spinicorne, 
Americorophium salmonis), which had extremely high abundances in several northern 
California locations, made up 54 % of total infaunal abundance in the study. Among the 
10 most abundant taxa at all study sites, nonindigenous and cryptogenic (species of 
uncertain geographic origin) species made up 6 % of total infaunal abundance. 

The 1999 Western Coastal EMAP study provides the first quantitative assessment of 
the condition of the small estuaries of Washington, Oregon and California. When these 
data are combined with the data collected in 2000 from the three largest estuarine 
systems on the West Coast (Puget Sound, Columbia River, San Francisco Bay), there 
will exist the first comprehensive data set for evaluating the overall condition of all 
estuarine systems of the West Coast. 


XVIII 


1.0 Introduction 


1.1 Program Background 

Safeguarding the natural environment is fundamental to the mission of the US 
Environmental Protection Agency (EPA). The legislative mandate to undertake this part 
of the Agency’s mission is embodied, in part, in the Clean Water Act (CWA). Sections of 
this Act require the states to report the condition of their aquatic resources and list those 
not meeting their designated use (Sections 305b and 303d, respectively). Calls for 
improvements in environmental monitoring date back to the late 1970’s, and have been 
recently reiterated by the General Accounting Office (GAO, 2000). The GAO report 
shows that problems with monitoring of aquatic resources continue to limit states’ 
abilities to carry out several key management and regulatory activities on water quality. 
At the national level, there is a clear need for coordinated monitoring of the nation’s 
ecological resources. As a response to these needs at state and national levels, the 
EPA Office of Research and Development (ORD) has undertaken research to support 
the Agency’s Regional Offices and the states in their efforts to meet the CWA reporting 
requirements. The Environmental Monitoring and Assessment Program (EMAP) is one 
of the key components of that research and EMAP-West is the newest regional 
research effort in EMAP. From 1999 through 2005, EMAP-West will seek to develop 
and demonstrate the tools needed to measure ecological condition of the aquatic 
resources in the 14 western states in EPA’s Regions 8,9, and 10. 

The Coastal Component of EMAP-West is a partnership with the states of California, 
Oregon and Washington, the National Oceanic and Atmospheric Administration, and the 
Biomonitoring of Environmental Status and Trends Program (BEST) of the U.S. 
Geological Survey, to measure the condition of the estuaries of these three states. 
Sampling began during the summer of 1999 and the initial phase of estuarine sampling 
was completed in 2000. Data from this program will be the basis for individual reports of 
condition for each state, and will be used to provide data to the National Coastal 
Assessment. 

The US EPA’s National Coastal Assessment (NCA) is a five-year effort led by EPA’s 
Office of Research and Development to evaluate the assessment methods it has 
developed to advance the science of ecosystem condition monitoring. This program will 
survey the condition of the Nation’s coastal resources (estuaries and offshore waters) 
by creating an integrated, comprehensive coastal monitoring program among the 
coastal states to assess coastal ecological condition. The NCA is accomplished 
through strategic partnerships with all 24 U.S. coastal states. Using a compatible, 
probabilistic design and a common set of survey indicators, each state conducts the 
survey and assesses the condition of its coastal resources independently. Because of 
the compatible design, these state estimates can be aggregated to assess conditions at 
the EPA Regional, biogeographical, and national levels. 


1 




This report provides a statistical summary of the data from the first year of sampling 
(1999) for the small estuarine systems of the states of Washington, Oregon, and 
California (excluding Puget Sound, the main channel of the Columbia River, and San 
Francisco Bay). 

1.2 The Western United States Context for a Coastal Condition Assessment 

Nationwide, growth of the human population is disproportionally concentrated in the 
coastal zone (Culliton et al., 1990). Within the coastal region of the western U.S., 
greatest population expansion has been in the major urban areas of Seattle, Portland, 
the San Francisco Bay area, and much of Southern California. These metro areas are 
either directly located on coastal water bodies or, like Portland, are on major rivers and 
thus influence the estuaries downstream. While development around the estuaries 
between north Puget Sound and Point Reyes, CA, has been less intense, substantial 
population growth is taking place across the region. Human population growth in the 
coastal zone of the west is a principal driver for many ecological stressors such as 
habitat loss, pollution, and nutrient enhancement which alter coastal ecosystems and 
affect the sustainability of coastal ecological resources (Copping and Bryant, 1993). 
Increased globalization of the economy is a major driver influencing the introduction of 
exotic species into ports and harbors. Major environmental policy decisions at local, 
state and federal levels related to land use planning, growth management, habitat 
restoration and resource utilization will determine the future trajectory for estuarine 
conditions of the western U.S. 

Changes associated with human population growth in the western coastal region tend to 
be most obvious in the larger, urban areas, but all coastal resources have been 
subjected to significant alterations over the last 150 years. In one of the earliest 
ecological alterations, sea otters, a known ecological keystone species (Simenstad et 
al., 1978), were largely removed from western coastal ecosystems by 1810, and 
populations have never recovered. The wave of western mining in the late 1800's had 
limited effects on most coastal systems in terms of altering estuaries or causing 
chemical pollution (Durning, 1996). Outside of the major ports, western estuaries are 
believed to have generally low concentrations of toxic pollutants because of relatively 
low population densities and low levels of heavy industry (Copping and Bryant, 1993), 
but data for most estuaries are sparse. 

Due to exploitative fishing in the Pacific Northwest, native oyster populations were 
largely wiped out by the late 1800's, and salmon catch peaked by the early 1900's 
(Durning, 1996). Resource exploitation for agriculture, logging and damming each 
resulted in massive changes to land use practices throughout the region. In the 
Chesapeake Bay region, deforestation associated with human settlement and 
agricultural clearing was shown to have led to a 100% increase in sediment 
accumulation rates (Cooperand Brush, 1991) during the 1800's. Sedimentation 
problems associated with land use changes may be especially acute along the West 
Coast north of San Francisco due to the combination of steep coastal watersheds, high 


2 


rainfall, and timber harvesting. Nutrient and sediment loadings from population centers 
will augment the increased flux of these materials resulting from the larger scale 
watershed alterations associated with logging of the coastal mountains (Howarth et al., 
1991). 

The increase in regional and international marine commerce along the West Coast has 
resulted in the introduction of nonindigenous species. The effect of nonindigenous 
species on estuarine habitats has only recently come under scrutiny (Carlton and 
Geller, 1993), but the potential for ecological transformation is great. Some 367 marine 
invertebrate taxa were recorded in the ballast water of ships arriving in Coos Bay, 
Oregon, from Japan (Carlton and Geller, 1993). In Washington state, the introduction of 
smooth cordgrass, Spartina alterniflora, has resulted in the conversion of hundreds of 
hectares of mud flat to salt marsh habitat with consequences to the ecosystem that 
have not yet been fully defined (Simenstad and Thom, 1995). 

Benthic environments are areas where many types of impacts from the stressors 
described above will tend to accumulate. Deposition of toxic materials, accumulation of 
sediment organics, and oxygen deficiency of bottom waters typically have a greater 
impact on benthic organisms than on planktonic and nektonic organisms because of 
their more sedentary nature. Long-term studies of the macrobenthos (Reish, 1986; 
Holland and Shaughnessey, 1986) demonstrate that macrobenthos are a sensitive 
indicator of pollutant effects. Benthic assemblages are also closely linked to both lower 
and higher trophic levels, as well as to processes influencing water and sediment 
quality, and therefore appear to integrate responses of the entire estuarine system 
(Leppakoski, 1979; Holland and Shaughnessey, 1986). 

Biologically, the EMAP Western Coastal study area is represented by two biogeographic 
provinces, the Columbian Province, which extends from the Washington border with 
Canada to Point Conception, California, and the Californian Province, which extends 
from Point Conception to the Mexican border. Within the biogeographic provinces there 
are also major transitions in the distribution of the human population. Major population 
centers occur in the southern end of Puget Sound, around San Francisco Bay, and 
generally surrounding most of the estuaries of southern California. In contrast, the 
region of coastline from north of San Francisco Bay through northern Puget Sound has 
a much lower population density. While it may be presumed that the magnitude of 
anthropogenic impacts will tend to show a similar distribution, this hypothesis has not 
yet been tested for West Coast estuaries. 

1.3 Objectives 

The EMAP sampling program conducted in the small estuaries of the West Coast in 
1999 was the first-year component of the larger EMAP Western Coastal Program, which 
has the following objectives: 


3 





1. To assess the condition of estuarine resources of Washington, Oregon and California 
based on a range of indicators of environmental quality using an integrated survey 
design; 

2. To establish a baseline for evaluating how the conditions of the estuarine resources 
of these states change with time; 

3. To develop and validate improved methods for use in future coastal monitoring and 
assessment efforts in the western coastal states; 

4. To transfer the technical approaches and methods for designing, conducting and 
analyzing data from probability based environmental assessments to the states and 
tribes. 


4 


2.0 Methods 


2.1 Sampling Design and Statistical Analysis Methods 

2.1.1 Background 

The EMAP approach to evaluating the condition of ecological resources is described in 
reports such as Diaz-Ramos et al. (1996), Stevens (1997), Stevens and Olsen (1999), 
and is also presented in summaries provided on the internet at the URL: 

http://www.epa.gov/nheerl/arm/index.htm 

A brief summary from these documents follows. 

Given that it is generally impossible to completely census an extensive resource such 
as the set of all estuaries on the West Coast, a more practical approach to evaluating 
resource condition is to sample selected portions of the resource using probability 
based sampling. Studies based on random samples of the resource rather than on a 
complete census are termed sample surveys. Sample surveys offer the advantages of 
being affordable, and of allowing extrapolations to be made of the overall condition of 
the resource based on the random samples collected. Survey methods are widely used 
in national programs such as forest inventories, agricultural statistics survey, national 
resource inventory, consumer price index, labor surveys, and such activities as voter 
opinion surveys. 

A survey design provides the approach to selecting samples in such a way that they 
provide valid estimates for the entire resource of interest. Designing and executing a 
sample survey involves five steps: (1) creating a list of all units of the target population 
from which to select the sample, (2) selecting a random sample of units from this list, (3) 
collecting data from the selected units, (4) summarizing the data with statistical analysis 
procedures appropriate for the survey design, and (5) communicating the results. The 
list or map that identifies every unit within the population of interest is termed the 
sampling frame. 

The sampling frame for the EMAP Western Coastal Program was developed from 
USGS 1:100,000-scale digital line graphs and stored as a GIS data layer in the 
ARC/INFO program. A series of programs and scripts (Bourgeois et al., 1998) was 
written to create a random sampling generator (RSG) that runs in ArcView. Site 
selection consisted of using the RSG to first overlay a user-defined sampling grid of 
hexagons over the spatial resource which consisted of all estuaries of the West Coast. 
The area of the hexagons was controlled by adjusting the distance to hexagon centers, 
and by defining how many sample stations were to be generated for each sampling 
region. After the sampling grid was overlaid on the estuarine resource, the program 
randomly selected hexagons and randomly located a sampling point within the hexagon. 
Only one sampling site was selected from any hexagon selected. The program 


5 






determined whether a sampling point fell in water or on land, and sites that fell on land 
were not included. The RSG was run iteratively until a hexagon size was determined 
which generated the desired number of sampling sites within the resource (Bourgeois et 
al., 1998). 

Hexagon size may be different for classes of estuarine systems of different areal extent. 
The final data analysis which provides the estimates of resource condition then weights 
the samples based on the area of the estuarine class. Stevens (1997) terms this a 
random tessellation stratified survey design applied to each estuarine resource class. 

2.1.2 Sampling Design 

2.1.2.1 1999 West Coast Design 

The assessment of condition of small estuaries conducted in 1999 was the first phase of 
a planned two-year comprehensive assessment of all estuaries of the states of 
Washington, Oregon and California. The complete assessment will require the 
integrated analysis of data collected from the smaller estuarine systems in 1999 and the 
larger estuarine systems in 2000. The intent of the design is to be able to combine data 
from all stations for analysis, using the inclusion probabilities, defined as the total 
estuarine area in km 2 within a given design stratum (= estuarine size class), to weight 
the representation of samples in the combined analysis. 

The West Coast sampling frame was constructed as a GIS coverage that would include 
the total area of the estuarine resource of interest. Available GIS coverages were not 
perfect representations of the estuarine resource, and so the coverages were defined to 
ensure that they included the resource, but may have possibly included some nearby 
land or inland water. The inland boundary of the sampling frame was defined as the 
head of salt water influence, while the seaward boundary was defined by the confluence 
with the ocean. Sample locations could fall within any water depth contained within the 
estuarine resource which was bounded by the shoreline. In some cases, extremely 
shallow sites were deemed inaccessible by field crews with the sampling gear specified 
(Section 2.6). Emergent salt marsh areas were not included in the sampling frame 
because the required indicators to deal with marsh habitats were not available. 

For the state of Washington, the 1999 design included only estuaries along the 
coastline outside of the Puget Sound system, and consisted of a total of 50 sites (Table 
2.1). Tributary estuaries of the Columbia River located within Washington state were 
included in the 1999 sampling effort, while the main channel area was not sampled until 
2000 (as part of the 2000 Oregon design). The sampling frame used three hexagonal 
grid sizes to cover the size range of estuaries: 0.86, 7.79, 36.58 km 2 . The hexagonal 
grid sizes were used to locate random sample sites within a total of four strata 
representing differing total areas of the estuarine resource in Washington (Table 2.1). 

To insure some level of sampling across the entire range of estuarine sizes, sampling 
effort was partitioned as 10 stations within the smallest estuarine size class, 25 stations 


6 


within the two strata representing the medium sized estuaries, and 15 stations in the 
largest size class. No alternate or oversample sites were included in the design. 

The Oregon 1999 design included only small estuaries of the state and consisted of 50 
sites. Tributary estuaries of the Columbia River located within Oregon were included in 
the 1999 sampling effort, while the main channel area was not sampled until 2000. The 
sampling frame for small estuaries utilized four hex sizes to cover the size range of 
estuaries: 1.24, 3.46, 4.58, and 7.28 km 2 . Approximately equal sampling effort was 
placed in each of the four estuarine strata, which represented differing size classes of 
estuaries, to insure some level of sampling across the entire range of estuarine sizes. 

An intensive sampling effort was also designed for Tillamook Bay, where a total of 30 
sites were selected using a hex size of 1.04 km 2 . No points from the base study design 
were placed in Tillamook Bay. All sites from both the base study and intensive study 
were combined for analysis. No alternate or oversample sites were included in the 
design. 

The 1999 California base study design included all estuaries of the state with the 
exception of San Francisco Bay, and consisted of a total of 50 sites. The sampling 
frame utilized three hexagonal grid sizes to cover the size range of estuaries in the 
sampling frame: 0.86, 7.79, and 12.50 km 2 . Approximately equal sampling effort was 
placed in each of the three estuarine size classes (<5, 5-25 and >25 km 2 ) to ensure 
some level of sampling across the entire range of estuarine sizes. No alternate or 
oversample sites were selected during the design, and thus any sites which could not 
be sampled were not replaced. 

The estuarine systems on the northern California coast, with the exception of the Areata 
and Humboldt Bay systems, are relatively poorly studied. A number of the rivers which 
discharge directly into the Pacific Ocean have been listed as failing to meet designated 
uses and have been designated for development of Total Maximum Daily Loadings 
(TMDL). At the request of the Region 9 Office of EPA, an intensive study was 
conducted to sample the river mouth estuaries of both TMDL listed and non-TMDL 
listed systems of Northern California. The purpose of this assessment was to determine 
if there was any difference in the estimates of condition for the two categories of 
estuarine resource. 

Using finer scale hexagonal grids, 30 sites were randomly selected at the mouths of the 
river systems in Northern California. The design for this intensive study incorporated 6 
differing hexagonal grid sizes: 0.0346, 0.0498, 0.0585, 0.0800, 0.0914, and 0.1060 km 2 . 
The hexagonal grid sizes were used to locate random sample sites within a total of 
seven strata representing differing total areas of the estuarine resource in these 
Northern California river mouth systems (Table 2-1). Sample sites were divided equally 
between streams with and without TMDL listings (Table 2-1). No alternate or 
oversample sites were selected during the design, and thus any sites which could not 
be sampled were not replaced. 


7 



While the intent of the California design was to be able to integrate all study sites 
seamlessly into combined analyses, an inadvertent design change occurred which 
somewhat complicates interpretation of results. In defining the target population for the 
Northern California sites, a restriction of sampling to a distance of 0.25 km from the 
estuarine mouth was imposed. This definition differs from that of the remainder of the 
West Coast assessment which used a target population defined by the head of salt in 
the estuary. In order to prevent duplicative sampling effort, the intensive study of 
northern California small river systems had been excluded from the frame for the base 
California study. Thus, a small area (approximately 10 km 2 ) representing the portion of 
the Northern California river systems excluded from the intensive study was 
inadvertently omitted from the California sampling frame. 

2.1.2.2 2000 West Coast Design 

While results of the 2000 sampling effort are not presented in this report, a description 
of the sample design for 2000 is provided in order to demonstrate the overall plan for 
the western coastal assessment effort. 

The Washington 2000 sampling design included only the large “estuary” of Puget 
Sound and its tributaries. Site selection for this estuary used a combined approach in 
order to allow collaboration with a survey previously conducted by NOAA under the 
NOAA National Status and Trends Program. The overall design combined the existing 
NOAA probability based, randomized monitoring design with the EMAP Western 
Coastal study design. The EMAP hexagonal grid was extended to include Canadian 
waters at the north end of Puget Sound, and then was overlaid on the existing NOAA 
monitoring sites. If a NOAA site fell within a hexagon, the site was designated as the 
EMAP sampling point. If not, a random site was selected based on the EMAP 
protocols. The design incorporated three different hex sizes, two covering most of the 
Puget Sound region (86.6, 250.28 km 2 ), and one used for intensifying in the region of 
the San Juan Islands (21.65 km 2 ). There were 41 stations selected based on the NOAA 
sampling stations, in addition to 30 new EMAP stations, of which 10 were associated 
with the San Juan Islands. No alternate or oversampling sites were included in the 
design frame. 

The Oregon 2000 design included only the main channel area of Columbia River. The 
Columbia River system was split into two subpopulations, the lower, saline portion and 
the upper, freshwater portion, with hex sizes of 13.85 and 5.4 km 2 and total numbers of 
stations of 20 and 30, respectively. No alternate or oversample sites were included in 
the design. 

The 2000 California design included only San Francisco Bay and its tributaries. Site 
selection for this estuary used a combined approach in order to allow collaboration with 
a survey being conducted by NOAA under the NOAA National Status and Trends 
Program. An EMAP sampling design was developed specifically for NOAA to implement 
a multiyear monitoring program to characterize condition of the small systems within the 


8 


San Francisco Bay. To insure complete coverage of the bay for the EMAP Western 
Coastal study, the NOAA design was augmented with a sampling design which split the 
Bay into two subpopulations (open bay and smaller surrounding systems). For the open 
bay, a hex size of 36.58 km 2 was used and 31 sites were generated. For the smaller 
systems, a different hexagon size (3.46 km 2 ) was used to generate 19 sites for 
sampling. This grid was overlaid on the newly designed NOAA small systems 
monitoring project. If a NOAA site fell within a hexagon, the site was used as the 
sampling point. If not, a random point was generated based on the standard 
randomization routines used by Western Coastal EMAP as part of the National Coastal 
Assessment. No alternate or oversample sites were selected. 


9 









DISCO 














HOKO RIVER 


MAKAHBAY 
OZETTE 
RIVER 

-h + 


DUNGENESS BAY 
FRESHWATER BAY 


WASHINGTON 


KALALOCH CREEK 
RAFT RIVER 

QUINAULT RIVER $ ® 


CONNER CREEK $ 
GRAYS HARBOR 


WILLAPA BAY 


COLUMBIA RIVER ESTUARIES 
(WASHINGTON) 


- 125 ° 


- 124 ° 


B Base Study Sites 0 Abandoned Sites 

SO 0 SO 100 ISO km 


Figure 2-1. Location of Washington EMAP survey sites. 


10 



















Figure 2-2. Location of EMAP survey sites along the northern portion of the Oregon 
coast, including survey sites for the intensification study of Tillamook Bay. 


11 













Figure 2-3. Location of EMAP survey sites along the southern portion of the Oregon 
coast. 


12 













Figure 2-4. Location of EMAP survey sites for the intensification study of Tillamook 
Bay, Oregon. 


13 













* 


o 

§ 


L 

V 

\ 

V 

SMITH RIVER (CA) • 


WILSON CREEK 
KLAMATH RIVER 

BIG LAGOON 


i 

I 
/ 

b' 

s 

I.ITTI.F. RIVER • 

ARCATABAY 0 
HUMBOLDT BAY ^ 

EEL RIVER • 

BEAR RIVER * 


r 




& 


/ 


Sv 


V 


NOYO RIVER 
CASPAR CREEK 
BIG RIVER 
ALBION RIVER 


/ 

i 


ELK CREEK ^ 
GARCIA RIVER • 


- 124 ° 


OREGON 




CALIFORNIA 


+ 


- 122 ° 

I 


Intensive Study Sites 


50 


0 


50 


$ Base Study Sites 

100 150 200 km 


Figure 2-5. Location of California EMAP survey sites in Northern California from the 
Oregon border to the Garcia River. 


14 



















Figure 2-6. Location of California EMAP survey sites in Northern and Central California 
from the Russian River to the Santa Ynez River. 


15 













o 


+ 


+ 


_ l _ 1J. 

SANTA BARBARA 9 

HARBOR VENTURA RIVER 
CHANNEL ISLANDS HARBOR 1 


CALIFORNIA 


$ 





. «■> 
<*> 






\ 


9 

POINT MUGU 
LAGOON 


KING HARBOR 


9 


m 

LOS ANGELES HARBOR ^ 

LONG BEACH HARBOR 


LOS ANGELES RIVER 




DANA POINT® 
HARBOR 


+ 


SANTA MARGARITA RIVER 


9 


AGUA HEDIONDA CREEK 


9 



SAN DIEGO RIVER 
SAN DIEGO BAY 


+ 



- 119 * 

9 Base Study Sites 


100 


o 


100 


- 117 ° 


200 km 


Figure 2-7. Location of California EMAP survey sites in Central and Southern California 
from Santa Barbara to the Mexican border. 


16 











Table 2-1. West Coast sampling sites with station coordinates of locations sampled. 
The northern California small estuary TMDL study sites are noted as either Y = TMDL 
Site, N = Non-TMDL Site. Frame area represents the total estuarine area within a 
stratum. An * in a station location indicates the site was abandoned prior to sampling. 


EMAP Sta. No. 

Latitude 

Longitude 

Estuary 

Hex 

Frame Area 

Stratum 

TMDL 





Size 

km 2 



WA99-0001 

48.320 

-124.680 

Makah Bay 

7.79 

77.288 

WA99-002 

N/A 

WA99-0002 

48.314 

-124.670 

Makah Bay 

7.79 

77.288 

WA99-002 

N/A 

WA99-0003 

48.305 

-124.671 

Makah Bay 

7.79 

77.288 

WA99-002 

N/A 

WA99-0004 

48.288 

-124.365 

Hoko River 

0.86 

8.363 

WA99-001 

N/A 

WA99-0005 

48.181 

-124.708 

Ozette River 

0.86 

8.363 

WA99-001 

N/A 

WA99-0006 

48.149 

-123.633 

Freshwater Bay 

7.79 

77.288 

WA99-002 

N/A 

WA99-0007 

48.148 

-123.601 

Freshwater Bay 

7.79 

77.288 

WA99-002 

N/A 

WA99-0008 

48.143 

-123.616 

Freshwater Bay 

7.79 

77.288 

WA99-002 

N/A 

WA99-0009 

48.160 

-123.148 

Dungeness Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0010 

48.079 

-122.900 

Discovery Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0011 

48.058 

-122.905 

Discovery Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0012 

48.021 

-122.859 

Discovery Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0013 

48.003 

-122.843 

Discovery Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0014 

47.997 

-122.874 

Discovery Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0015 

47.606 

-124.373 

KalalochCreek 

0.86 

8.363 

WA99-001 

N/A 

WA99-0016 

47.463 

-124.339 

Raft River 

0.86 

8.363 

WA99-001 

N/A 

WA99-0017 

47.347 

-124.298 

Quinault River 

7.79 

77.288 

WA99-002 

N/A 

WA99-0018 

* 

★ 

Quinault River 

7.79 

77.288 

WA99-002 

N/A 

WA99-0019 

47.089 

-124.176 

Conner Creek 

0.86 

8.363 

WA99-001 

N/A 

WA99-0020 

47.004 

-124.040 

Grays Harbor 

36.58 

562.230 

WA99-004 

N/A 

WA99-0021 

47.005 

-124.000 

Grass Creek 

0.86 

8.363 

WA99-001 

N/A 

WA99-0022 

46.966 

-123.951 

Grays Harbor 

36.58 

562.230 

WA99-004 

N/A 

WA99-0023 

46.940 

-124.104 

Grays Harbor 

36.58 

562.230 

WA99-004 

N/A 

WA99-0024 

46.935 

-124.028 

Grays Harbor 

36.58 

562.230 

WA99-004 

N/A 

WA99-0025 

46.967 

-123.858 

Grays Harbor 

36.58 

562.230 

WA99-004 

N/A 

WA99-0026 

46.921 

-124.067 

Grays Harbor 

36.58 

562.230 

WA99-004 

N/A 

WA99-0027 

46.873 

-124.034 

Beardslee Slough 

0.86 

8.363 

WA99-001 

N/A 

WA99-0028 

46.870 

-124.022 

Beardslee Slough 

0.86 

8.363 

WA99-001 

N/A 

WA99-0029 

46.848 

-124.032 

Grays Harbor 

36.58 

562.230 

WA99-004 

N/A 

WA99-0030 

46.715 

-124.045 

Willapa Bay 

36.58 

562.230 

WA99-004 

N/A 

WA99-0031 

46.704 

-123.887 

Willapa Bay 

36.58 

562.230 

WA99-004 

N/A 

WA99-0032 

★ 

* 

Willapa Bay 

36.58 

562.230 

WA99-004 

N/A 

WA99-0033 

46.650 

-124.012 

Willapa Bay 

36.58 

562.230 

WA99-004 

N/A 

WA99-0034 

46.567 

-123.942 

Willapa Bay 

36.58 

562.230 

WA99-004 

N/A 

WA99-0035 

46.539 

-123.924 

Willapa Bay 

36.58 

562.230 

WA99-004 

N/A 

WA99-0036 

46.418 

-123.418 

Willapa Bay 

36.58 

562.230 

WA99-004 

N/A 

WA99-0037 

★ 

★ 

Willapa Bay 

36.58 

562.230 

WA99-004 

N/A 

WA99-0038 

46.310 

-124.009 

Baker Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0039 

46.301 

-124.026 

Baker Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0040 

46.273 

-123.973 

Baker Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0041 

* 

* 

Grays River 

0.86 

8.363 

WA99-001 

N/A 

WA99-0042 

46.263 

-123.998 

Baker Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0043 

46.302 

-123.711 

Grays Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0044 

46.300 

-123.698 

Grays Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0045 

46.295 

-123.703 

Grays Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0046 

46.287 

-123.727 

Grays Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0047 

46.275 

-123.717 

Grays Bay 

7.79 

111.478 

WA99-003 

N/A 

WA99-0048 

46.095 

-122.922 

Cowlitz River 

7.79 

77.288 

WA99-002 

N/A 

WA99-0049 

46.085 

-122.880 

Carrolls Channel 

7.79 

77.288 

WA99-002 

N/A 

WA99-0050 

45.947 

-122.786 

Martin Slough 

0.86 

8.363 

WA99-001 

N/A 

OR99-0001 

46.188 

-123.912 

Youngs Bay 

3.46 

43.192 

OR99-003 

N/A 

OR99-0002 

46.211 

-123.724 

Cathlamet Bay 

3.46 

43.192 

OR99-003 

N/A 

OR99-0003 

46.180 

-123.865 

Youngs Bay 

3.46 

43.192 

OR99-003 

N/A 

OR99-0004 

46.217 

-123.672 

Cathlamet Bay 

3.46 

43.192 

OR99-003 

N/A 

OR99-0005 

46.167 

-123.893 

Youngs Bay 

3.46 

43.192 

OR99-003 

N/A 

OR99-0006 

46.208 

-123.688 

Cathlamet Bay 

3.46 

43.192 

OR99-003 

N/A 

OR99-0007 

46.169 

-123.872 

Youngs Bay 

3.46 

43.192 

OR99-003 

N/A 

OR99-0008 

46.226 

-123.588 

Marsh Island Creek 

1.24 

13.578 

OR99-001 

N/A 

OR99-0009 

46.190 

-123.744 

Cathlamet Bay 

3.46 

43.192 

OR99-003 

N/A 


17 







OR99-0010 

46.189 

-123.746 

Cathlamet Bay 

3.46 

43.192 

OR99-003 

N/A 

OR99-0011 

46.186 

-123.681 

Cathlamet Bay 

3.46 

43.192 

OR99-003 

N/A 

OR99-0012 

46.149 

-123.817 

Youngs River 

7.28 

99.605 

OR99-002 

N/A 

OR99-0013 

46.187 

-123.592 

Knappa Slough 

1.24 

13.578 

OR99-001 

N/A 

OR99-0014 

46.170 

-123.144 

Bradbury Slough 

7.28 

99.605 

OR99-002 

N/A 

OR99-0015 

46.134 

-123.272 

Wallace Slough 

7.28 

99.605 

OR99-002 

N/A 

OR99-0016 

46.129 

-123.226 

Clatskanie River 

1.24 

13.578 

OR99-001 

N/A 

OR99-0017 

46.123 

-123.036 

Rinearson Slough 

1.24 

13.578 

OR99-001 

N/A 

OR99-0018 

45.691 

-123.899 

Nehalem River 

7.28 

99.605 

OR99-002 

N/A 

OR99-0019 

45.394 

-123.953 

Netarts Bay 

7.28 

99.605 

OR99-002 

N/A 

OR99-0020 

45.197 

-123.961 

Nestucca River 

1.24 

13.578 

OR99-001 

N/A 

OR99-0021 

45.166 

-123.944 

Little Nestucca River 

1.24 

13.578 

OR99-001 

N/A 

OR99-0022 

45.040 

-123.994 

Salmon River 

1.24 

13.578 

OR99-001 

N/A 

OR99-0023 

44.925 

-124.018 

Siletz Bay 

7.28 

99.605 

OR99-002 

N/A 

OR99-0024 

44.622 

-124.034 

Yaquina Bay 

7.28 

99.605 

OR99-002 

N/A 

OR99-0025 

44.599 

-124.016 

Yaquina River 

7.28 

99.605 

OR99-002 

N/A 

OR99-0026 

44.574 

-123.963 

Yaquina River 

7.28 

99.605 

OR99-002 

N/A 

OR99-0027 

44.414 

-123.999 

Alsea River 

1.24 

13.578 

OR99-001 

N/A 

OR99-0028 

44.305 

-124.115 

Yachats River 

1.24 

13.578 

OR99-001 

N/A 

OR99-0029 

44.188 

-124.036 

Rock Creek 

1.24 

13.578 

OR99-001 

N/A 

OR99-0030 

44.011 

-124.126 

Siuslaw River 

7.28 

99.605 

OR99-002 

N/A 

OR99-0031 

44.022 

-123.881 

Siuslaw River 

7.28 

99.605 

OR99-002 

N/A 

OR99-0032 

44.740 

-124.136 

Umpqua River 

4.58 

59.163 

OR99-004 

N/A 

OR99-0033 

43.762 

-124.005 

Smith River (OR) 

7.28 

99.605 

OR99-002 

N/A 

OR99-0034 

43.725 

-124.146 

Umpqua River 

4.58 

59.163 

OR99-004 

N/A 

OR99-0035 

44.772 

-123.903 

Smith River (OR) 

7.28 

99.605 

OR99-002 

N/A 

OR99-0036 

43.722 

-124.124 

Umpqua River 

4.58 

59.163 

OR99-004 

N/A 

OR99-0037 

43.693 

-124.100 

Scholfield Creek 

1.24 

13.578 

OR99-001 

N/A 

OR99-0038 

43.692 

-124.065 

Umpqua River 

4.58 

59.163 

OR99-004 

N/A 

OR99-0039 

43.423 

-124.246 

Coos Bay 

4.58 

59.163 

OR99-004 

N/A 

OR99-0040 

43.414 

-124.207 

Coos Bay 

4.58 

59.163 

OR99-004 

N/A 

OR99-0041 

43.406 

-124.218 

Coos Bay 

4.58 

59.163 

OR99-004 

N/A 

OR99-0042 

43.386 

-124.292 

Coos Bay 

4.58 

59.163 

OR99-004 

N/A 

OR99-0043 

43.404 

-124.199 

Coos Bay 

4.58 

59.163 

OR99-004 

N/A 

OR99-0044 

43.368 

-124.304 

Coos Bay 

4.58 

59.163 

OR99-004 

N/A 

OR99-0045 

43.341 

-124.320 

South Slough 

7.28 

99.605 

OR99-002 

N/A 

OR99-0046 

43.370 

-124.148 

Coos River 

1.24 

13.578 

OR99-001 

N/A 

OR99-0047 

43.377 

-124.108 

Coos River 

1.24 

13.578 

OR99-001 

N/A 

OR99-0048 

43.350 

-124.169 

Catching Slough 

1.24 

13.578 

OR99-001 

N/A 

OR99-0049 

43.321 

-124.154 

Catching Slough 

1.24 

13.578 

OR99-001 

N/A 

OR99-0050 

42.423 

-124.419 

Rogue River 

7.28 

99.605 

OR99-002 

N/A 

OR99-0051 

45.552 

-123.929 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0052 

45.547 

-123.935 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0053 

45.551 

-123.912 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0054 

45.534 

-123.935 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0055 

45.539 

-123.923 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0056 

45.536 

-123.932 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0057 

45.538 

-123.906 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0058 

45.528 

-123.929 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0059 

45.531 

-123.912 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0060 

45.524 

-123.929 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0061 

45.517 

-123.934 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0062 

45.524 

-123.912 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0063 

45.511 

-123.921 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0064 

45.517 

-123.891 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0065 

45.509 

-123.933 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0066 

45.515 

-123.901 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0067 

45.503 

-123.933 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0068 

45.509 

-123.911 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0069 

45.511 

-123.891 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0070 

45.498 

-123.887 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0071 

45.506 

-123.895 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0072 

45.498 

-123.908 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0073 

45.497 

-123.891 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0074 

45.491 

-123.894 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0075 

45.501 

-123.869 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0076 

45.495 

-123.894 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0077 

45.491 

-123.900 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0078 

45.481 

-123.900 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0079 

45.468 

-123.885 

Tillamook Bay 

1.04 

33.732 

OR99-005 

N/A 

OR99-0080 

45.441 

-123.877 

Tillamook River 

1.04 

33.732 

OR99-005 

N/A 


18 




CA99-0001 

41.162 

-124.118 

Big Lagoon 

7.79 

102.651 

CA99-002 

N/A 

CA99-0002 

40.837 

-124.117 

Areata Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0003 

40.824 

-124.142 

Areata Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0004 

40.720 

-124.238 

Humboldt Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0005 

40.703 

-124.258 

Humboldt Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0006 

38.287 

-123.028 

Bodega Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0007 

38.263 

-123.012 

Bodega Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0008 

38.249 

-122.978 

Bodega Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0009 

38.104 

-122.848 

Tomales Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0010 

38.015 

-122.917 

Drakes Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0011 

38.006 

-122.910 

Drakes Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0012 

38.006 

-122.873 

Drakes Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0013 

38.002 

-122.865 

Drakes Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0014 

36.961 

-122.019 

Santa Cruz Harbor 

7.79 

102.651 

CA99-002 

N/A 

CA99-0015 

36.859 

-121.801 

Pajaro River 

0.86 

13.837 

CA99-003 

N/A 

CA99-0016 

36.633 

-121.845 

Monterey Harbor 

7.79 

102.651 

CA99-002 

N/A 

CA99-0017 

36.628 

-121.853 

Monterey Harbor 

7.79 

102.651 

CA99-002 

N/A 

CA99-0018 

36.537 

-121.930 

Carmel Bay 

7.79 

102.651 

CA99-002 

N/A 

CA99-0019 

36.525 

-121.936 

Carmel Bay 

7.79 

102.651 

CA99-002 

N/A 

CA99-0020 

35.346 

-120.847 

Morro Bay 

7.79 

102.651 

CA99-002 

N/A 

CA99-0021 

35.318 

-120.858 

Morro Bay 

7.79 

102.651 

CA99-002 

N/A 

CA99-0022 

35.171 

-120.737 

San Luis Obispo Bay 

7.79 

102.651 

CA99-002 

N/A 

CA99-0023 

35.173 

-120.725 

San Luis Obispo Bay 

7.79 

102.651 

CA99-002 

N/A 

CA99-0024 

35.161 

-120.710 

San Luis Obispo Bay 

7.79 

102.651 

CA99-002 

N/A 

CA99-0025 

34.692 

-120.597 

Santa Ynez River 

0.86 

13.837 

CA99-003 

N/A 

CA99-0026 

34.407 

-119.693 

Santa Barbara Harbor 

0.86 

13.837 

CA99-003 

N/A 

CA99-0027 

34.354 

-119.309 

Ventura River 

0.86 

13.837 

CA99-003 

N/A 

CA99-0028 

34.180 

-119.230 

Channel Islands Harbor 

0.86 

13.837 

CA99-003 

N/A 

CA99-0029 

34.167 

-119.227 

Channel Islands Harbor 

0.86 

13.837 

CA99-003 

N/A 

CA99-0030 

34.097 

-119.079 

Point Mugu Lagoon 

0.86 

13.837 

CA99-003 

N/A 

CA99-0031 

33.844 

-118.395 

King Harbor 

0.86 

13.837 

CA99-003 

N/A 

CA99-0032 

33.777 

-118.242 

Los Angeles River 

0.86 

13.837 

CA99-003 

N/A 

CA99-0033 

33.742 

-118.252 

Los Angeles Harbor 

12.5 

268.504 

CA99-001 

N/A 

CA99-0034 

33.755 

-118.154 

Long Beach Harbor 

7.79 

102.651 

CA99-002 

N/A 

CA99-0035 

33.741 

-118.177 

Long Beach Harbor 

7.79 

102.651 

CA99-002 

N/A 

CA99-0036 

33.730 

-118.256 

Los Angeles Harbor 

12.5 

268.504 

CA99-001 

N/A 

CA99-0037 

33.743 

-118.140 

Long Beach Harbor 

7.79 

102.651 

CA99-002 

N/A 

CA99-0038 

33.724 

-118.214 

Los Angeles Harbor 

12.5 

268.504 

CA99-001 

N/A 

CA99-0039 

33.719 

-118.233 

Los Angeles Harbor 

12.5 

268.504 

CA99-001 

N/A 

CA99-0040 

33.461 

-117.702 

Dana Point Harbor 

0.86 

13.837 

CA99-003 

N/A 

CA99-0041 

33.234 

-117.412 

Santa Margarita River 

0.86 

13.837 

CA99-003 

N/A 

CA99-0042 

33.145 

-117.342 

Agua Hedionda Creek 

0.86 

13.837 

CA99-003 

N/A 

CA99-0043 

33.143 

-117.339 

Agua Hedionda Creek 

0.86 

13.837 

CA99-003 

N/A 

CA99-0044 

32.772 

-117.210 

Mission Bay 

7.79 

102.651 

CA99-002 

N/A 

CA99-0045 

32.755 

-117.248 

San Diego River 

0.86 

13.837 

CA99-003 

N/A 

CA99-0046 

32.759 

-117.219 

San Diego River 

0.86 

13.837 

CA99-003 

N/A 

CA99-0047 

32.727 

-117.215 

San Diego Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0048 

32.726 

-117.180 

San Diego Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0049 

32.651 

-117.129 

San Diego Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0050 

32.639 

-117.138 

San Diego Bay 

12.5 

268.504 

CA99-001 

N/A 

CA99-0051 

41.945 

-124.201 

Smith River (CA) 

0.10 

0.654 

CA99-006 

N 

CA99-0052 

41.947 

-124.204 

Smith River (CA) 

0.106 

0.654 

CA99-006 

N 

CA99-0053 

41.944 

-124.197 

Smith River (CA) 

0.106 

0.654 

CA99-006 

N 

CA99-0054 

41.941 

-124.196 

Smith River (CA) 

0.106 

0.654 

CA99-006 

N 

CA99-0055 

41.937 

-124.196 

Smith River (CA) 

0.106 

0.654 

CA99-006 

N 

CA99-0056 

41.606 

-124.100 

Wilson Creek 

0.08 

0.014 

CA99-004 

N 

CA99-0057 

41.605 

-124.101 

Wilson Creek 

0.08 

0.014 

CA99-004 

N 

CA99-0058 

41.547 

-124.081 

Klamath River 

0.0346 

0.309 

CA99-009 

Y 

CA99-0059 

41.546 

-124.075 

Klamath River 

0.0346 

0.309 

CA99-009 

Y 

CA99-0060 

41.541 

-124.079 

Klamath River 

0.0346 

0.309 

CA99-009 

Y 

CA99-0061 

41.028 

-124.112 

Little River 

0.08 

0.018 

CA99-005 

N 

CA99-0062 

41.027 

-124.109 

Little River 

0.08 

0.018 

CA99-005 

N 

CA99-0063 

40.644 

-124.305 

Eel River 

0.0914 

0.219 

CA99-010 

Y 

CA99-0064 

40.646 

-124.304 

Eel River 

0.0914 

0.219 

CA99-010 

Y 

CA99-0065 

40.475 

-124.388 

Bear River 

0.08 

0.018 

CA99-005 

N 

CA99-0066 

39.427 

-123.808 

Noyo River 

0.0585 

0.427 

CA99-007 

Y 

CA99-0067 

39.417 

-123.812 

Hare Creek 

0.08 

0.018 

CA99-005 

N 

CA99-0068 

39.418 

-123.809 

Hare Creek 

0.08 

0.018 

CA99-005 

N 

CA99-0069 

39.361 

-123.815 

Caspar Creek 

0.08 

0.014 

CA99-004 

N 

CA99-0070 

39.303 

-123.794 

Big River 

0.0585 

0.427 

CA99-007 

Y 


19 








CA99-0071 

39.226 

-123.770 

Albion River 

0.0914 

0.219 

CA99-010 

Y 

CA99-0072 

39.225 

-123.768 

Albion River 

0.0914 

0.219 

CA99-010 

Y 

CA99-0073 

39.227 

-123.764 

Albion River 

0.0914 

0.219 

CA99-010 

Y 

CA99-0074 

39.103 

-123.707 

Elk Creek 

0.08 

0.014 

CA99-004 

N 

CA99-0075 

39.102 

-123.705 

Elk Creek 

0.08 

0.014 

CA99-004 

N 

CA99-0076 

38.954 

-123.730 

Garcia River 

0.0585 

0.427 

CA99-007 

Y 

CA99-0077 

38.451 

-123.127 

Russian River 

0.0498 

0.104 

CA99-008 

Y 

CA99-0078 

38.449 

-123.125 

Russian River 

0.0498 

0.104 

CA99-008 

Y 

CA99-0079 

38.307 

-122.995 

Estero Americano 

0.0585 

0.427 

CA99-007 

Y 

CA99-0080 

38.270 

-122.976 

Estero San Antonio 

0.0585 

0.427 

CA99-007 

Y 


20 



2.2 Data Analysis 

Analysis of indicator data was conducted by calculation of cumulative distribution 
functions (CDFs), an analysis approach that has been used extensively in other EMAP 
coastal studies (Summers et al., 1993; Strobel et al.,1994; Hyland et al., 1996). The 
CDFs describe the full distribution of indicator values in relation to their areal extent 
across the sampling region of interest. The approximate 95% confidence intervals for 
the CDFs also were computed based on estimates of variance. A detailed discussion of 
methods for calculation of the CDFs used in EMAP analyses is provided in Diaz-Ramos 
et al. (1996). 

The Horvitz-Thompson ratio estimate of the CDF is given by the formula: 


F(x„) = 


/(y,<x*) 

M n\ 


N 


A " 

A/ = Z 


/=1 


1 


7Ti 


F(x u) = estimated CDF (proportion) for indicator value x„ 

n = number of samples 

y,= the sample response for site i 

x* = the k th CDF response indicator 


l(y < x*) = 


1, y < x* 

0, otherwise 
m - selection probability for site i 


N = the estimated population size 


The selection probability for a site is 1/area of the hexagon, e.g. the hexagon area of 
California estuaries in the base study in the size class 5-25 km 2 . When calculating the 
mean for a variable, the same equation is used with Y, replacing the indicator function. 


21 







The Horvitz-Thompson unbiased estimate of the variance for the ratio estimate is given 
by the formula: 



N = , d, = l(y < x.) - F(x .), d / = l(y< x„) - F(x.) 


A 


F(xk) = estimated CDF (proportion) for indicator value x* 



1, y, < Xk 
0, otherwise 


Xk = the k th indicator level of interest 
y = value of indicator for the i th unit sampled 
7r j = inclusion density evaluated at the location 
of the i th sample point 

Ttfj = joint inclusion density evaluated at the locations 

of the i th and j th sample points 
n = number of units sampled 


The joint inclusion probabilities are given by 


(n 1 ) * -,~j 


n 


22 







When estimating the CDF across several strata, the above estimates for each stratum 
must be combined. The equations are 



F(x k ) = estimated CDF 


F^Xk) = estimated CDF for stratum i 
Af = area for stratum i 
S = number of strata 
A = total area of all strata 


and the variance estimate across strata is 



V = estimated variance for all strata 


V t = estimated variance for stratum i 
A, = area for stratum i 
S = number of strata 
A = total area of all strata 


23 





2.3 Indicators 


The condition of West Coast estuarine resources was evaluated by collecting data for a 
standard set of environmental parameters at all stations within the survey (Table 2-2). 
Field procedures followed methods outlined in the USEPA National Coastal Assessment 
Field Operations Manual (USEPA, 2001b). The environmental indicators were similar to 
those used in previous EMAP estuarine surveys in other regions of the country 
(Weisberg et al., 1992; Macauley et al., 1994, 1995; Strobel et al., 1994, 1995; Hyland 
et al., 1996, 1998). Indicators were divided into those representing general habitat 
condition (Habitat Indicators), condition of benthic and demersal faunal resources (Biotic 
Condition Indicators), and exposure to pollutants (Exposure Indicators). Habitat 
indicators describe the general physical and chemical conditions at the study site, and 
are often important in providing information used to interpret the results of biotic 
condition indicators (e.g., salinity and sediment grain size with regard to benthic 
community composition). Biotic condition indicators are measures of the status of the 
benthic biological resources in response to site environmental conditions. The 
Exposure indicators used in this survey quantify the amounts and types of pollutant 
materials (metals, hydrocarbons, pesticides) that may be harmful to the biological 
resources present. Some indicators may overlap the above categories. For example, 
dissolved oxygen is clearly an indicator of habitat condition, but may also be considered 
an exposure indicator because of the potentially harmful effects of low dissolved oxygen 
levels to many members of the benthic community. 

In addition to the core set of indicators, a number of supplemental indicators were 
conducted either by EMAP or by external collaborators during the EMAP Western 
Coastal survey (Table 2-3). An additional sediment toxicity test was conducted for the 
California stations composing the base study. The amphipod Eohaustorius estuarius 
acute toxicity test was used in order to compare the sensitivity of this species with 
Ampelisca abdita, which is the most commonly used amphipod bioassay species in the 
EMAP program. Scientists with the USGS/BEST program conducted two sediment 
porewater toxicity tests using the sea urchin Arbacia punctulata (fertilization toxicity test, 
embryo development toxicity test) (USGS, 2000), and conducted the H4IIE bioassay 
(bioassay-derived 2,3,7,8-tetrachlorodibenzo - p -dioxin equivalents (TCDD-EQ)) for 
exposure offish to planar halogenated hydrocarbons (USGS, 2001). Results of the sea 
urchin bioassay tests are included in the present report, while the details of the H4lle 
bioassay are provided in USGS (2001). Results of the Eohaustorius toxicity test are not 
presented here, since this test was done only with California sediments, but will be 
provided in a separate statistical data report for the state of California. 


24 


Table 2-2. Core environmental indicators for the EMAP Western Coastal survey. 


Habitat Indicators 

Salinity 
Water depth 
pH 

Water temperature 
Total suspended solids 
Chlorophyll a concentration 

Nutrient concentrations (nitrates, 

nitrites, ammonia, & phosphate) 

Percent light transmission 

Secchi depth 

Percent silt-clay of sediments 

Percent total organic carbon (TOC) 
in sediments 


Benthic Condition Indicators 

Infaunal species composition 

Infaunal abundance 

Infaunal species richness and diversity 

Demersal fish species composition 

Demersal fish abundance 

Demersal fish species richness and 
diversity 

External pathological anomalies in fish 

Exposure Indicators 

Dissolved oxygen (DO) concentration 
Sediment contaminants 
Fish tissue contaminants 

Sediment toxicity (Ampelisca abdita 
acute toxicity test) 


25 









Table 2-3. Environmental indicators under development or conducted by collaborators 
during the EMAP Western Coastal survey. 


Benthic Condition Indicators 

West Coast benthic infaunal index - EMAP 


Exposure Indicators 

Sediment toxicity (amphipod Eohaustorius estuarius acute toxicity test) - EMAP 
(California only) 


Sediment porewater toxicity (sea urchin Arbacia punctulata fertilization toxicity test) - 
USGS/BEST 1 


Sediment porewater toxicity (sea urchin Arbacia punctulata embryo development 
toxicity test) - USGS/BEST 1 


H4IIE Bioassay-derived 2,3,7,8-tetrachlorodibenzo - p -dioxin equivalents (TCDD-EQ) 
for exposure offish to planar halogenated hydrocarbons - USGS/BEST 2 


1 USGS, 2000 

2 USGS, 2001 


26 





2.3.1 Water Measurements 


2.3.1.1 Hydrographic Profile 

Water column profiles were performed at each site to measure dissolved oxygen (DO), 
salinity, temperature, pH, and depth. Both secchi depth and a measurement of light 
attenuation using photosynthetically active radiation (PAR) were made at each station. 
Methods and procedures used for hydrographic profiling follow guidance provided in the 
NCA Quality Assurance Project Plan document (US EPA, 2001). 

Basic water quality parameters were measured by different instruments in each state. 
Washington field crews used the Seabird SBE 19 CTD with data logging capability. In 
Oregon there were two field crews. The Oregon Dept, of Environmental Quality field 
crew used a YSI 6920 datasonde. The field crew provided by National Marine Fisheries 
Service used a Hydrolab datasonde. California used a Hydrolab Datasonde 4a with a 
cable connection to a deck display. Prior to conducting a CTD (Conductivity, 
Temperature, Depth) cast, the instrument was allowed 2-3 minutes of warmup while 
being maintained near the surface, after which the instrument was slowly lowered at the 
rate of approximately 1 meter per second during the down cast. Individual 
measurements were made at discrete intervals (with sufficient time for equilibration) as 
follows: 

Shallow sites (< 2 m) - 0.5-m intervals; 

Typical depths (>2<10 m) - 0.5 m (near-surface) and every 1-m interval to near¬ 
bottom (0.5 m off-bottom); 

Deep sites (>10 m) - 0.5 m (near-surface) and every 1-m interval to 10 m, then at 
5-m intervals, thereafter, to near-bottom (0.5 m off-bottom). 

Near-bottom conditions were measured at 0.5 m above the bottom by first ascertaining 
whether the instrument was on the bottom (slack line/cable), and then pulling it up 
approximately 0.5 m. A delay of 2-3 minutes was used to allow disturbed conditions to 
settle before taking the near-bottom measurements. The profile was repeated on the 
ascent and recorded for validation purposes, but only data from the descent were 
reported in the final data. 

Measurements of light penetration were recorded using a hand-held LiCor LI-1400 light 
meter for conditions at discrete depth intervals in a manner similar to that for profiling 
water quality parameters with the hand-held water quality probes. The underwater 
sensor was hand lowered according to the regime described above and at each discrete 
interval, the deck reading and underwater reading were recorded. If the light 
measurements became negative before reaching bottom, the measurement was 
terminated at that depth. The profile was repeated on the ascent. As an indicator of 
water column light conditions, the transmissivity at 1 m depth was calculated. 


27 









The California field crew measured ambient light data in two ways. The Hydrolab 
datasonde unit had a LiCor spherical irradiance sensor (LI -193SA) mounted to the 
sensor package. For boat deployments, the deck sensor recording ambient light was a 
cosine collector (LI-190SA)). However, many of the California sample locations were 
too shallow to allow sampling from a boat, and required walking in to the sample site. At 
these stations, the field crew took ambient irradiance with the spherical sensor in air, 
and then took several subsurface readings with the same sensor. The difference in 
geometry between the deck reference sensor and submerged sensor was corrected for 
during the analysis of light transmission. An empirical comparison of similar LiCor 
spherical and flat sensors, both calibrated for air measurements, was conducted. The 
spherical sensor collected an average of two times the light measured by the flat 
sensor. All ambient light measurements for California stations sampled by boat were 
first corrected by this factor. The minimum depth where the first submerged light 
reading was taken varied widely among stations, which made inter-station comparison 
difficult. Therefore, the submerged and corresponding in air light measurements, 
together with the depth of the measurement, were used to compute the light extinction 
coefficient k, using the relationship k = (ln(l 0 ) - ln(l d ))/d , where l 0 = in air measure of 
light, l d = submerged light, and d = the depth of the first submerged light measurement. 
The value of k that was computed was assumed to characterize the light attenuation 
down to a depth of 1m, and light at a depth of 1 m (l 1m ) was then calculated as l 1m = e ( " 
kd) , where d = 1m. Percent light transmission at 1m was then computed as (l 1m /1 0 ) * 100. 

Secchi depth was determined by using a standard 20-cm diameter black and white 
secchi disc. The disc was lowered to the depth at which it could no longer be discerned, 
then was slowly retrieved until it just reappeared. The depth of reappearance was 
recorded as secchi depth (rounded to the nearest 0.5 m). 

2.3.1.2 Water Quality Indicators 

The water column was sampled at each site for dissolved nutrients (N and P species), 
chlorophyll a concentration, and total suspended solids (TSS). Sampling varied slightly 
among the states but generally followed the guidance provided in the NCA Quality 
Assurance Project Plan document (US EPA, 2001). At shallow sites (<2 m), water 
samples were taken at 0.5 m (near-surface) and 0.5 m off-bottom. If the depth was so 
shallow that the near-surface and near-bottom overlapped, then only a mid-depth 
sample was taken. For sites deeper than 2 m, samples were taken at 0.5 m (near¬ 
surface), mid-depth, and 0.5 m off-bottom. 

For TSS analysis, 1 liter of unfiltered seawater was collected at the depths described 
above. The samples were held in 1-L polypropylene bottles on wet ice in the field and 
stored at 4°C until analyzed. 

For Washington samples, water used for nutrient, chlorophyll, and dissolved oxygen 
samples was collected from discrete depths using 1.7-liter Nisken bottle and transferred 
to two 66-ml plastic bottles. The chlorophyll samples were filtered by placing them in a 


28 


funnel containing a 0.7-(jm GFF filter attached to a receiving bottle. A hand pump was 
used to pull the seawater past the filter and into a receiving flask. The GFF filter was 
then folded in half and placed in a labeled glass centrifuge tube containing 10 ml of 90 
% acetone, and placed on ice until the tubes could be frozen at the end of the day. A 
0.45-pm syringe filter was used with a pre-cleaned, 60-ml plastic syringe to filter 
approximately 40 ml of water for nutrient analyses into 60-ml plastic bottles. 

In California, samples were obtained by using a Wildco 1.2-liter stainless steel 
Kemmerer sampler. A second water sample was collected from each of the same 
depths and an approximately 1-liter subsample was poured into a clean, wide-mouth 
polycarbonate container for the chlorophyll and nutrient analyses. Two disposable, 
graduated 50-cc polypropylene syringes fitted with a stainless steel or polypropylene 
filtering assembly were used to filter the water sample through 0.7-pm GFF filters, and 
the volume of water (up to 200 ml for each syringe) filtered was recorded. Both filters 
were carefully removed using tweezers, folded once upon the pigment side, placed in a 
prelabeled, disposable petri dish, and capped. The petri dish was wrapped in aluminum 
foil, placed in a small styrofoam ice chest with several pounds of dry ice, and kept 
frozen until analyzed. The syringe and filtering assembly were washed with deionized 
water and stored in a clean compartment between sampling stations. For nutrients, 
approximately 40 ml of filtrate from the chlorophyll filtration (surface water) were 
collected into two prelabeled, clean 60-ml Nalgene screw-capped bottles, stored in the 
dry ice chest, and kept frozen on dry ice until analyzed. 

Dissolved Oxygen was measured at Washington stations with a Beckman DO sensor 
deployed on the Seabird CTD, at Oregon stations with a Yellow Springs Instruments 
model 6562 DO sensor on the YSI datasonde, and at California stations with a Hydrolab 
DO sensor on the Hydrolab datasonde. 

2.3.2 Sediment Toxicity Testing 

2.3.2.1 Sediment Collection for Toxicity Testing, Chemical Analysis and Grain Size 

Combined sediment for toxicity testing and chemical analysis was collected at all sites 
from the top 2-3 centimeters of surficial sediment. Procedures for sediment collection 
followed the guidance provided in the NCA Quality Assurance Project Plan document 
(US EPA, 2001). Where possible, sediment grabs were taken with a 0.1-m 2 van Veen 
sampler. The top 2-3 centimeters of surficial sediment were scooped from each 
individual grab, composited in a pre-cleaned container and homogenized within the 
container by thorough stirring. Sediment from 2-9 grabs was composited to collect 
approximately 6 liters of sediment. Where station depth precluded sampling with a boat 
and van Veen grab, the sampling crew walked in to the sample site, and the top 2-3 cm 
of sediment at the site was scooped from the sediment surface and processed similarly 
to sediment collected by grab. This occurred at the following stations: 4 sites in 
Washington: WA99-0015, WA99-0016, WA99-0017, WA99-0019; 33 sites in California: 


29 




CA99-0001, CA99-0015, CA99-0021, CA99-0025, CA99-0030, CA99-0037, CA99-0041, 
CA99-0045-46, CA99-0051-57, CA99-0059-65, CA99-0067-71, CA99-0073-74, CA99- 
0076, CA99-0079-80. The composited sediment was held on ice and distributed to 
individual containers for toxicity testing and chemical analyses either on board the 
research vessel or at the laboratory. Aliquots of the homogenized sediment were 
distributed to pre-cleaned containers for analysis of sediment organics, trace metals, 
grain size and toxicity testing. Toxicity-test sediment was held at 4°C to await initiation of 
toxicity testing within 7 days of collection. 

2.3.2.2 Laboratory Test Methods 

2.3.2.2.1 Amphipod Toxicity Tests 

The 10-day, solid-phase toxicity test with the marine amphipod Ampelisca abdita was 
used to evaluate potential toxicity of sediments from all sites. Procedures followed the 
general guidelines provided in ASTM Protocol El367-92 (ASTM, 1991), the EPA 
amphipod sediment toxicity test manual (USEPA, 1994a) and the EMAP Laboratory 
Methods Manual (USEPA, 1994b). The Ampelisca test is a 10-d acute toxicity test which 
measures the effect of sediment exposure on amphipod survival under static aerated 
conditions. 

Approximately 3-3.5 L of surface sediments (composite of upper 2-3 cm from multiple 
grabs) were collected from the sampling sites and stored in glass or polyethylene jars at 
4 °C in the dark until testing. Toxicity tests were conducted with subsamples of the same 
sediment on which the analysis of organic and trace metal contaminants and other 
sediment characteristics was performed. 

Ampelisca abdita were collected from the Narrow (=Pettaquamscutt) River, Rhode 
Island, by Eastern Aquatic Biosupply, or from San Pablo Bay in the San Francisco 
Estuary by Brezina and Associates. Amphipods were shipped via overnight carrier to the 
Marine Pollution Studies Laboratory at Granite Canyon, CA (CA and WA sediments), 
Southern California Coastal Water Research Project (SCCWRP - CA sediments) or the 
Northwestern Aquatic Sciences, Inc., laboratory in Newport, Oregon (OR sediments), 
where the Ampelisca tests were conducted. Amphipods were acclimated for 2-9 days 
prior to testing. During the acclimation period, the amphipods were not fed (WA and CA) 
or were fed a commercially available dried algal mix (OR). Healthy juvenile amphipods of 
approximately the same size (0.5-1.0 mm) were used to initiate tests. The general health 
of each batch of amphipods was evaluated in a reference toxicity test (i.e., “positive 
control”), which was run for 96 h in a dilution series with seawater (no sediment phase) 
and the reference toxicants cadmium chloride or sodium dodecyl sulfate (SDS). LC 50 
values for reference toxicants were computed for comparison with other reported toxicity 
ranges for the same reference toxicant and test species. 


30 


Treatments for the definitive tests with field samples consisted of five replicates of each 
field sediment sample (100% sediment) and a negative control. A negative control was 
run with each batch of field samples, which ranged from 4 to18 samples per batch. 
Control sediment was ambient sediment from the amphipod collection sites. Twenty 
amphipods were randomly distributed to each of five replicates per each treatment 
including the control. Amphipods were not fed during the tests. All tests were 
conducted under static conditions with aeration, and were monitored for water quality 
(temperature, salinity, dissolved oxygen, pH, and total ammonia in the overlying water). 
Target test temperature for A. abdita was 20 °C and target salinity was 28 psu. 

The negative controls provided a basis of comparison for determining statistical 
differences in survival in the field sediments. In addition, control survival provided a 
measure of the acceptability of final test results. Test results with A. abdita were 
considered valid if mean control survival (among the 5 replicates) was not less than 90% 
and survival in no single control replicate was less than 80%. Test batches where these 
QA requirements were not met were not included in the CDF analysis. 

One-liter glass containers with covers were used as test chambers. Each chamber was 
filled with 200 ml of sediment and 600-800 ml of filtered seawater. The sediment was 
press-sieved, through either a 1.0-mm screen for control samples or a 2.0-mm screen for 
field samples, to remove ambient fauna prior to placing the sediment in a test chamber. 
Light was held constant during the 10-day test to inhibit amphipod emergence from the 
sediment, thus maximizing exposure to the test sediment. 

At the conclusion of a test, the sediment from each chamber was sieved through a 0.5- 
mm screen to remove amphipods. The number of animals dead, alive, or missing was 
recorded. Sediments with >10% missing animals were re-examined under a dissecting 
microscope to ensure that no living specimens had been missed. Amphipods still 
unaccounted for were considered to have died and decomposed in the sediment. 

A variety of quality control procedures were incorporated to assure acceptability of 
amphipod test results and comparability of the data with other studies. As described 
above, these provisions included the use of standard ASTM and EMAP protocols, 
positive controls run with a reference toxicant, negative “performance” controls run with 
reference sediment from the amphipod collection site, and routine monitoring of water 
quality variables to identify any departures from optimum tolerance ranges. 

2.3.2.2.2 Sea Urchin Toxicity Tests 

The Biomonitoring and Environmental Status and Trends Program (BEST) of the U.S. 
Geological Survey obtained sediment samples collected by EMAP and conducted two 
types of sea urchin toxicity tests. The fertilization and embryological development toxicity 
tests were conducted with sediment porewater using gametes of the sea urchin Arbacia 
punctulata. Methods and results are described in a technical report (USGS, 2000). 


31 










Sediments for testing were held on ice or refrigerated at 4°C and shipped in insulated 
coolers within 7 days to the BEST laboratory. Pore water was extracted from the test 
sediments within 24 hours of receipt using a pneumatic device, centrifuged to remove 
suspended particulate material, then stored frozen. Sediments that were received by the 
BEST laboratory at temperatures exceeding acceptable temperature criteria were 
excluded from the CDF analysis. 

Sediment pore water was thawed two days prior to testing and stored at 4°C. Water 
quality parameters (salinity, temperature, DO) were measured in the thawed pore water 
and adjusted if necessary. Samples were tested at a temperature and salinity of 20 + 2°C 
and 30 + Ipsu. Other water quality parameters that were measured included dissolved 
oxygen, pH, sulfide, ammonia and dissolved organic carbon. 

Toxicity was determined using percent fertilization and embryological development 
(percent normal pluteus stage) as endpoints with gametes of the sea urchin Arbacia 
punctulata. A seawater dilution series (100, 50 and 25%) was used to determine the 
toxicity of the sediment porewater samples. Filtered seawater and reconstituted brine 
were used as dilution blanks. Reference pore water from an uncontaminated site in 
Redfish Bay, TX, was included in each test as a negative control. A dilution series with 
sodium dodecyl sulfate was used as a positive control. Toxicity was determined with 
statistical comparisons among treatments using ANOVA and Dunnett’s one-tailed t-test 
on the arcsine square root transformed data. 

2.3.3 Biotic Condition Indicators 

2.3.3.1 Benthic Community Structure 

Sediment samples to enumerate the benthic infauna were collected at all sampling sites 
unless rocky bottom or other factors prohibited obtaining a benthic sample (see section 
2.6). Procedures followed the guidance provided in the NCA Quality Assurance Project 
Plan document (US EPA, 2001). The standard sampling gear for all three states was a 
0.1-m 2 van Veen grab sampler. All Oregon sites were sampled using this gear. In both 
Washington and California, some stations in shallow water required modified methods 
when field crews walked into the site. In California, sites with a water depth less than 
approximately 1 meter were sampled with hand-held cores. At these shallower areas, a 
composite of sixteen 0.0065-m 2 cores was taken, for a total surface area of 0.1-m 2 . Eight 
of the base California stations and 23 of the Northern California intensive sites were 
sampled with these cores. To evaluate the efficiency of smaller sample sizes, a single 
0.0065-m 2 core was taken from the van Veen grabs at 24 sites in Southern California. 

For this analysis, the results from the sub-cores and the remainder of the van Veen grab 
were combined. In Washington, four shallow-water sites (WA99-0015, WA99-0016, 
WA99-0017, WA99-0019) were sampled using a 5-gallon bucket sampler with an area of 
0.049 m 2 . Because of the difference in area, these four samples were excluded from the 
analysis of benthic community structure. 


32 


The majority of the grab and core samples penetrated a minimum of 5 cm deep. The 
eleven samples that penetrated 3-4 cm are included in the present analysis. After 
collection, samples were sieved through nested 0.5-mm and 1.0-mm mesh screens. An 
elutriation process was used to minimize damage to soft-bodied animals and the material 
retained on the screens was relaxed in 1 kg of MgS04 per 20 L of seawater for 30 
minutes. The residue was then preserved in the field in sodium borate-buffered 10% 
formalin. 

The preserved samples were sent to analytical laboratories where they were transferred 
to 70% ethanol within 2 weeks of field collection. The 1.0-mm mesh screen samples 
were then sorted from the debris. The 0.5-mm mesh samples were not included as part 
of EMAP West and were not sorted. The organisms were then identified to the lowest 
practical taxonomic level (most often species), and counted by the primary taxonomists 
(see Table 2-10). Secondary QA taxonomists ensured that uniform nomenclature was 
used across the entire Western Coastal EMAP region; these recognized taxonomic 
experts identified and resolved taxonomic discrepancies among the sets of primary 
taxonomists. In the analyses for this report, all insect taxa were grouped as Insecta. 
Individual insect taxa will be identified in later versions of the database. 

The benthic infaunal data were used to compute total numbers of individuals and total 
number of species per 0.1-m 2 sample. The Shannon-Weaver information diversity index 
H' was calculated (log base 2) per 0.1-m 2 sample. Species were classified as native, 
nonindigenous, cryptogenic, or indeterminate. Cryptogenic species are species of 
uncertain geographic origin (Carlton, 1996), while indeterminate taxa are those taxa not 
identified to a sufficiently low level to classify as native, nonindigenous, or cryptogenic 
(Lee et al., in press). Species were classified using Cohen and Carlton (1995) as the 
primary source and a report by TN and Associates (2001) for taxa not classified by Cohen 
and Carlton. The TN and A report specifically classified the benthic species collected by 
the 1999 EMAP survey as native, nonindigenous, or cryptogenic. 

2.3.3.2 Fish Trawls 

Fish trawls were conducted at each site, where possible, to collect fish/shellfish for 
community structure and abundance estimates, collect target species for contaminant 
analyses, and collect specimens for histopathological examination. In some cases, it was 
necessary to use beach seines instead of trawls to collect fish for tissue analysis. Only 
trawls were used to evaluate fish community structure because consistency between 
beach seines was impossible to maintain. 

Trawls were conducted by using a 16-ft otter trawl with 1.5-inch mesh in the body and 
wings and 1.25-inch mesh in the cod end. Community structure data (i.e, the fish data on 
richness and abundance and individual lengths) were based on a trawl(s) of 10 minute 
duration. In open water, the trawl was conducted in a straight line with the site location 
near center. Timing of the trawl began after the length of towline had been payed out and 
the net began its plow. The speed over bottom was approximately 2 knots. When 


33 








possible, trawling was conducted for the entire 10-minute period, after which the ship’s 
transmission was placed in neutral and the trawl net retrieved and brought aboard. In 
constrained areas where 10-minute trawls were not possible, two 5-minute trawls were 
conducted. Contents of the bag were emptied into an appropriately sized trough or 
livebox to await sorting, identifying, measuring, and sub-sampling. Trawling was the last 
field activity performed because of possible disturbance to conditions at the site. Every 
effort was made to return any rare or endangered species back to the water before they 
suffered undue stress. 

In Oregon and Washington, fish for tissue and histopathological analysis were collected 
with a 120-foot long beach seine where waters were too shallow to use the otter trawl. 
The seine had 1-inch mesh in the wings and 3/8-inch mesh in the bag end. In California, 
a 100-foot seine with 1/8-inch mesh was used for fish collections in shallow waters. 

2.3.3.3 Fish Community Structure 

Fish from a successful trawl (full time on bottom with no hangs or other interruptions) 
were first sorted by species and identified to genus and species. Up to thirty individuals 
per species were measured by using a fish measuring board to the nearest centimeter 
(fork length when tail forked, otherwise overall length - snout to tip of caudal). The lengths 
were recorded on a field form and a total count made for each species. All fish not 
retained for histopathology or tissue chemistry were returned to the estuary. 

2.3.3.4 Fish Contaminant Sampling 

Several species of demersal soles, flounders, and dabs were designated as target 
species for the analyses of chemical contaminants in whole-body tissue. These flatfish 
are common along the entire U.S. Pacific Coast and are intimately associated with the 
sediments. Where the target flatfish species were not collected in sufficient numbers, 
perchiform species were collected. These species live in the water column but feed 
primarily or opportunistically on the benthos. In cases where neither flatfish species nor 
perches were collected, other species that feed primarily or opportunistically on the 
benthos were collected for tissue analysis. A total of 16 species were collected for tissue 
analysis in the base study sites in all three states and a total of 17 species if the intensive 
study stations are included. The species analyzed for tissue contaminants were (species 
occurring in no or only one base study station are identified): 

Pleuronectiformes 

Citharichthys sordidus - Pacific sanddab 

Citharichthys stigmaeus - speckled sanddab 

Paralichthys californicus - California halibut 

Platichthys stellatus - starry flounder 

Pleuronectes isolepis - butter sole (1 base study station OR) 

Pleuronectes vetulus - English sole 


34 


Psettichthys melanostictus - sand sole 

Symphurus atricauda - California tonguefish (1 base study station CA) 

Perciformes 

Cymatogaster aggregata - shiner perch 

Embiotoca lateralis - stripped sea perch (1 base study station OR) 
Gasterosteus aculeatus - threespine stickleback (1 base study and 
1 intensive study station CA) 

Genyonemus lineatus - white croaker 

Paralabrax maculatofasciatus - spotted sand bass (1 base study station CA) 
Paralabrax nebulifer- barred sand bass 


Other 

Atherinops affinis - topsmelt (1 base station CA) 

Leptocottus armatus - Pacific staghorn sculpin 

Oligocottus rimensis - saddleback sculpin (2 Northern CA intensive study stations) 

At sites where target species were captured in sufficient numbers, 3 to 30 individuals of a 
species were combined into a composited sample. Due to their small size, up to 220 
individual Gasterosteus aculeatus (threespine stickleback) were composited to obtain a 
sufficient tissue sample at one of the intensive sites in California. In all cases, the fish 
were first measured and recorded on the sampling form as chemistry fish. The fish were 
then rinsed with site water, individually wrapped with heavy duty aluminum foil (with the 
length of each individual fish printed on the foil wrap to facilitate the possible later 
selection of specific individuals at the laboratory), and placed together in a plastic, Ziploc 
bag labeled with the Station ID Code and a Species ID Code (e.g., the first four letters of 
both the genus and species). The fish tissue chemistry samples were held on wet ice in 
the field until they were transferred to shore and frozen to await laboratory analysis. 

2.3.3.5 Fish Contaminant Chemistry Analyses 

Neutral organic and metal contaminants were measured in the whole-body tissues of the 
seventeen species offish listed above (Section 2.4.3.4). Contaminant concentrations 
were determined for each of the composited tissue samples. A total of 11 metals, 20 
polychlorinated biphenyls (PCBs), DDT and its primary metabolites, and an additional 13 
pesticides were measured in the fish samples. Oregon measured PCB 110 and PCB77 
as PCB 110/77. Compounds not measured in all three states (e.g., PCB187) are not 
reported here. PAHs were not measured in fish tissues because of their rapid 
metabolism in vertebrates. The analytes measured in all three states in fish and 
sediments are summarized in Table 2-4. Table 2-5 summarizes the sample collection, 
preservation, and holding time requirements for sediment and tissue samples. Table 2-6 
summarizes the analytical methods used in the three states for both sediments and 
tissues. For tissue chemistry analyses, the NCA Quality Assurance Program Plan (EPA 
2001) recommended that internal standards known as surrogates be run, and suggested 
that reported concentrations for analytes be adjusted to correct for recovery of 


35 









surrogates. The state analytical laboratories generally used surrogates only as an 
indication of whether a re-extraction of a sample was required. 


2.3.3.6 Fish Gross Pathology 

Any fish pathologies (e.g., tumors) observed on fish collected in the trawls were 
photographed, then excised and placed into labeled pathology containers, and put 
immediately into Dietrich’s solution. Excised tissue included the entire pathology and 
some adjacent healthy tissue. Pathology information, including cartridge number, fish 
species, size, station ID, trawl number, pathology location, description, and sample depth 
was recorded onto a Cumulative Fish Pathology Log. At the end of the field collection, all 
samples were sent to Dr. Mark Meyers at NMFS/NOAA in Seattle for analysis. A 
separate fish pathology report will be prepared by NOAA. 


2.3.4 Sediment Chemistry 

A total of 15 metals, 20 PCB congeners (PCBs), DDT and its primary metabolites, 12 
pesticides, 21 polynuclear aromatic aromatics (PAHs), and total organic carbon (TOC) 
were measured in sediments in all three states (Table 2-4). Oregon measured PCB 110 
and PCB77 as PCB 110/77. Compounds not measured in all three states (e.g., 
hexaclorobenzene) are not reported here. With a few additions, this suite of compounds 
is the same as measured in the NOAA NS&T Program. 

Sediment for chemical analysis was collected from the top 2-3 centimeters in benthic 
grabs and stored in pre-cleaned glass containers (see Table 2-5). Sediment samples for 
chemical analysis were taken from the same sediment composite used for the sediment 
toxicity tests. Approximately 250-300 ml of sediment was collected from each station for 
analysis of the organic pollutants and another 250-300 ml for analysis of the metals and 
TOC (Table 2-5). Table 2-6 lists the analytical methods used for each compound. For 
sediment chemistry analyses, the NCA Quality Assurance Program Plan (EPA 2001) 
recommended that internal standards known as surrogates be run, and suggested that 
reported concentrations for analytes be adjusted to correct for recovery of surrogates. 

The state analytical laboratories generally used surrogates only as an indication of 
whether re-extraction of a sample was required. The exception was the laboratory for the 
State of Washington which made surrogate recovery corrections to the reported values 
for PAHs only. 


36 


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c 

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0 

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0 

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0 

CNJ 

0 

s_ 

3 

0 

E 

0 

JD 

0 

1 - 

■0 

0 

0 

0 

0 

E 



37 


















Table 2-5. Summary of EMAP-Coastal chemistry sample collection, preservation, and holding time requirements for 
sediment and fish tissues. Modified from Table 5-3 (U.S. EPA, 2001a). 



c 

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38 




Table 2-6. Methods used to analyze for contaminants in sediments and tissues. 
NA = not analyzed. 


Analyte 

CA 

Sediment/Tissue 

OR 

Sediment/Tissue 

WA 

Sediment/Tissue 

Aluminum 

ICPMS/ICPMS 

ICPAES/ICPAES 

ICPAES/ICPAES 

Antimony 

ICPMS/ICPMS 

GFAA/NA 

ICPMS/NA 

Arsenic 

ICPMS/ICPMS 

ICPAES/ICPAES 

AA/AA 

Cadmium 

ICPMS/ICPMS 

GFAA/GFAA 

ICPMS/ICPMS 

Chromium 

ICPMS/ICPMS 

ICPAES/ICPAES 

ICPAES/ICPMS 

Copper 

ICPMS/ICPMS 

ICPAES/ICPAES 

ICPAES/ICPMS 

Iron 

FAA/NA 

ICPAES/ICPAES 

ICPAES/ICPAES 

Lead 

ICPMS/ICPMS 

ICPAES/GFAA 

ICPMS/ICPMS 

Manganese 

ICPMS/ICPMS 

ICPAES/NA 

ICPAES/NA 

Mercury 

FIMS/FIMS 

CVAA/CVAA 

CVAA/CVAA 

Nickel 

ICPMS/ICPMS 

ICPAES/ICPAES 

ICPAES/ICPMS 

Selenium 

HAA/ICPMS 

HAA/HAA 

AA/AA (FURNACE) 

Silver 

GFAA/ICPMS 

GFAA/GFAA 

ICPMS/ICPMS 

Tin 

ICPMS/NA 

ICPAES/ICPAES 

ICPMS/ICPMS 

Zinc 

ICPMS/ICPMS 

ICPAES/ICPAES 

ICPAES/ICPMS 

PCB congeners 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

DDT, DDD, and 
DDE 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

PAHs 

GCMS/NA 

GCMS/NA 

GCMS/NA 

Aldrin 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

Alpha-Chlordane 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

Dieldrin 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

Endosulfan 1 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

Endosulfan II 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 


39 


Table continued on next page 










Endosulfan 

Sulfate 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

Endrin 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

Heptachlor 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

Fleptachlor 

Epoxide 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

Lindane 

(gamma-BFIC) 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

Mi rex 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

Trans-Nonachlor 

GCMS/GCMS 

GCECD/GCECD 

GCECD/GCECD 

TOC 

MARPCN l/NA 

EPA415.1/NA 

PSEP-TOC/NA 

Percent fines 

wet sieve/NA 

gravimetric/NA 

PSEP86/NA 


Analytical Methods: CVAA = cold vapor atomic absorption, FAA = flame atomic 
absorption, FIMS = flow injection mercury system, GCECD = gas chromatography with 
electron capture detection, GCMS = gas chromatography/mass spectroscopy, GFAA = 
graphite furnace atomic absorption spectrometry, ICPAES = inductively coupled 
plasma/atomic emission spectrometry, ICPMS = inductively coupled plasma/mass 
spectrometry , FIAA = hydride atomic absorption, MARPCN I = high temperature 
combustion method. 


40 





2.4 Quality Assurance/ Quality Control 

The quality assurance/quality control (QA/QC) program for the Western Coastal EMAP 
program is defined by the “Environmental Monitoring and Assessment Program (EMAP): 
National Coastal Assessment Quality Assurance Project Plan 2001-2004" (US EPA, 
2001a). The NCA has established Data Quality Objectives (DQO) for estimates of 
current status for indicators of condition which are stated as: "For each indicator of 
condition, estimate the portion of the resource in degraded condition within ±10% for the 
overall system and ±10% for subregions (i.e., states) with 90% confidence based on a 
completed sampling regime." An assessment of this standard for the combined 
1999/2000 data from the states of Washington, Oregon and California is presented in the 
Quality Assurance Appendix of the National Coastal Condition Report II (EPA, 2004). 

The level of uncertainty for the combined west coast data set for all major indicators was 
< 5%. 


In general, the quality assurance elements for the EMAP Western Coastal program 
included initial training workshops on all sampling and analysis requirements and initial 
laboratory capability exercises, program-wide audits of field and laboratory operations, 
documentation of chain-of-custody, and maintaining open lines of communication and 
information exchange. Information management needs were demonstrated to all 
participants by the Western Coastal EMAP information manager. Other quality control 
measures were incorporated to assure data reliability and comparability and are 
described in the NCA plan. These include the use of standard NCA protocols, routine 
instrument calibrations, measures of analytical accuracy and precision (e.g., analysis of 
standard reference materials, spiked samples, and field and laboratory replicates), 
measures of the quality of test organisms and overall data acceptability in sediment 
bioassays (e.g., use of positive and negative controls), range checks on the various types 
of data, cross-checks between original data sheets (field or lab) and the various 
computer-entered data sets, and participation in intercalibration exercises. 

Accuracy is used to estimate systematic error (measured vs. true or expected), while 
precision is used to determine random error (variability between individual 
measurements). Collectively, they provide an estimate of the total error or uncertainty 
associated with an individual measured value. Measurement quality objectives (MQO) for 
all NCA field and laboratory parameters are expressed in terms of accuracy, precision, 
and completeness goals in the NCA QA Project Plan (US EPA, 2001a, Table A7-1). 

These MQOs were established from considerations of instrument manufacturers 
specifications, scientific experience, and/or historical data. However, accuracy and 
precision goals may not be definable for all parameters due to the nature of the 
measurement type (e.g., fish pathology, no expected value). 


41 


2.4.1 QA of Chemical Analyses 

Details of the quality assurance procedures used to generate chemical concentrations 
within both sediments and tissue samples with acceptable levels of precision and 
accuracy are given in U.S. EPA (2001a). Briefly, a performance-based approach was 
used, which depending upon the compound included 1) continuous laboratory evaluation 
through the use of Certified Reference Materials (CRMs) and/or Laboratory Control 
Materials (LCMs), 2) laboratory spiked sample matrices, 3) laboratory reagent blanks, 

4) calibration standards, and 5) laboratory and field replicates. 

Control limit criteria for “relative accuracy” were based on comparing the laboratory’s 
value to the true or “accepted” values in CRMs or LCMs (see U.S. EPA, 2001a for 
details). The specific requirements for PAHs and PCBs/pesticides are that the “Lab’s 
value should be within ±30% of true value on average for all analytes; not to exceed 
±35% of true value for more than 30% of individual analytes.” (U.S. EPA 2001a). In 
addition to evaluating the individual PAH and PCB analytes, relative accuracy for total 
PAHs and PCBs was determined for each combined group of organic compounds. Metals 
and other inorganic compounds were treated individually, and the laboratory's value for 
each analyte should be within ±20% of the upper or lower 95% confidence limit of the 
CRM or LCM. Because of inherent variability at low concentrations, these control limit 
criteria were applied only to analytes having CRM or LCM values >10 times the MDL. 

To evaluate precision, each laboratory periodically analyzed CRM or LCM samples using 
a control limit of 3 standard deviations of the mean (Taylor, 1987). Based on analysis of 
all the samples in a given year, an overall relative standard deviation (RSD, or coefficient 
of variation) of less than 30% was considered acceptable precision for analytes with 
CRM concentrations > 10 times the MDL. 

In order to evaluate the MQOs for precision, various analytical quality assurance/quality 
control (QA/QC) samples were used, field measurement procedures were followed, and 
field vouchers were collected. For analytical purposes, Method Detection Limits (MDL’s) 
were calculated for the detection of each analyte at low levels distinguished above 
background noise, taking into consideration the relative sensitivity of an analytical 
method, based on the combined factors of instrument signal, sample size, and sample 
processing steps. The MDL is defined as “the minimum concentration of a substance 
that can be measured and reported with 99% confidence that the analyte concentration 
is greater than zero and is determined from analysis of a sample in a given matrix 
containing the analyte." (Code of Federal Regulations 40 CFR Part 136). Approved 
laboratories were expected to perform in general accord with the target MDLs presented 
for NCA analytes (US EPA, 2001a, Table A7-2). Because of analytical uncertainties 
close to the MDL, there is greater confidence with concentrations above the Reporting 
Limit (RL), which is the concentration of a substance in a matrix that can be reliably 
quantified during routine laboratory operations. Typically, RLs are 3 to 5 times the MDL. 
Concentrations between the MDL and the RL were used in generating the CDF and 


42 


mean for the analyte. Values below the MDL were set to 0 and this value was used in 
calculating both the CDFs and means. 

Table 2-7 lists the units, method detection limits (MDL), and reporting limits (RL) for each 
compound measured in sediment samples in all three states. The analytical methods 
are those used in the NOAA NS&T Program (Lauenstein and Cantillo, 1993) or 
documented in the EMAP-E Laboratory Methods Manual (U.S. EPA, 1993). The target 
MDLs for the National Coastal Assessment (US EPA, 2001a) were achieved in almost 
90% of sediment analytes across the three states (Table 2-7). Exceedances of the 
target MDL could potentially affect the frequency with which a compound is detected, but 
would have little effect on the shape of the CDF since such exceedances occur at the 
low end of the concentration distribution. 

Table 2-8 lists the units, method detection limits (MDL), and reporting limit (RL) for the 
tissue analytes. The target MDLs for the National Coastal Assessment (US EPA, 2001a) 
were achieved in over 90% of tissue analytes across the three states (Table 2-8). As 
mentioned for the sediments, exceedances of the target MDL could potentially affect the 
frequency with which a compound is detected, but would have little effect on the shape 
of the CDF since such exceedances occur at the low end of the concentration 
distribution. 

Prior to analysis of 1999 field samples, state laboratories participating in the NCA 
program performed a demonstration of capability using SRMs provided by EPA. Results 
of this exercise are described in EPA (2004, Appendix A). In summary, results were 
deemed acceptable for Washington and California and marginal for Oregon. 

A post-analysis assessment of the success of the analytical laboratories in meeting NCA 
QA/QC guidelines was conducted by the QA officer of the Western Ecology Division. 
These results are summarized in Table 2-9. Accuracy of results as assessed by 
comparison to either an SRM, CRM, or LCM was within guidelines for all states for 
analysis of metals in both sediment and tissues. For sediment PCBs and pesticides, 
performance of the Oregon laboratory was less than the desired level, and the 
performance of the California laboratories, while acceptable, was based on a limited 
number of analytes in the LCM. For sediment PAHs, performance of the Oregon 
laboratory was acceptable based on the LCM and less than desired based on the SRM. 
In several cases, accuracy could not be assessed for the field samples because 
laboratories did not analyze reference tissue material for PCBs (Washington) or 
pesticides (Washington, California), although ability to meet standards was 
demonstrated in the initial lab capability exercise. 

The NCA analytical laboratory accuracy standards are based on the evaluation of 
individual analytes (e.g. PCB congeners) while the NCA sediment condition indicators 
are based on total sediment or tissue PAFIs and PCBs. If the total PCB concentration in 
the SRM is compared to the estimated total recovery of PCBs in sediments for all 
congeners by the Oregon laboratory, the values are within 16% . A similar analysis for 

43 


Continued on page 50 






Table 2-7. Units, method detection limits (MDL), and reporting limits (RL) for sediment chemistry for compounds measured 
in all three states. The method detection limits and the reporting limits for Oregon and Washington are means of all the 
reported sediment values, including non-detects. Target MDLs are from the National Coastal Assessment (US EPA, 
2001a). NR = not reported. NA = not applicable. 



44 












Table 2-8. Units, method detection limits (MDL), and reporting limits (RL) for tissue chemistry for compounds measured in 
all three states. The reporting limits for Oregon and Washington are means of all the reported tissue values, including non- 
detects. The reporting limits for the PCBs in Oregon and Washington are mean of all the congeners. The PCB reporting 
limits in California are the range in individual congeners. Target MDLs are from the National Coastal Assessment (US 
EPA, 2001a). NA = not applicable. 



46 







47 





Table 2-9. Summary of performance of state analytical laboratories with regard to QA/QC criteria for analysis of reference 
materials, matrix spike recoveries, and relative percent differences (RPD) of duplicates. MS = matrix spike, SRM = 
Standard Reference Material, CRM = Certified Reference Material, LCM = Laboratory Reference Material, NA = not 
analyzed. 



48 














o 

■ 4 —» 

03 

O 

TO 

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TO 

C 

TO 

03 

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.Q 

TO 

Q) 

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TO 


TO 

E 


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—I 03 

iS 

C §• 
03 £: 

Q3 E 
03 

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? 03 

> _TO 

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* * 


49 










the recovery of total PAHs in sediments versus the SRM by the Oregon lab was within 
24%. These values are within ± 30% of the true value and are considered adequate for 
the purpose of inclusion of the Oregon total PCB and total PAH data in the computation 
of a regional CDF. 


2.4.2 QA of Taxonomy 

Quality control of taxonomic identifications involved the establishment of a network of 
secondary QA/QC taxonomic specialists who confirmed identifications made by the 
primary taxonomists (Table 2-10), and provided standardization of identifications among 
the state participants. 

In order to assure uniform taxonomy and nomenclature among the primary taxonomists 
for each group, and to avoid problems with data standardization at the end of the 
project, progressive QA/QC and standardization were implemented. At frequent, 
regular intervals (i.e., monthly), as primary taxonomy was completed, vouchers, voucher 
sheets, and a portion of the QA samples were sent to the QA taxonomists. Immediate 
feedback from the QA taxonomists to the primary taxonomists was used to correct work 
and standardize between regional taxonomists. Each voucher was accompanied by a 
voucher sheet listing the following information: major taxon (e.g., Annelida), family, 
genus, species, sample from which the specimen was taken; references used in the 
identification; and any characteristics of the specimen that differ from the original 
description. Provisional species were described in detail on the voucher sheet. 

As voucher specimens and bulk samples were processed by the QA taxonomist, any 
differences in identifications or counts were discussed and resolved with the primary 
taxonomist. The original data set remained with the primary taxonomist, and changes 
agreed upon between the primary and QA taxonomists were made by the primary 
taxonomist on a copy of the original data set. Changes to the data based on QA/QC 
analysis were tracked in writing by both the primary and QA taxonomists. 


50 


Table 2-10. Listing of primary and QA/QC taxonomists by taxon and region for the 1999 
Western Coastal EMAP study. 


Organisms 

QA/QC 

Taxonomist 

Primary 

Taxonomists 

Region* 

Annelida 

Gene Ruff 

John Oliver 

NC 



Larry Lovell 

SC 



Gene Ruff 

WO 



Kathy Welch 

WO 

Arthropoda 

Don Cadien 

Peter Slattery 

NC 



Tony Phillips 

SC 



Jeff Cordell 

WO 

Mollusca 

Don Cadien 

Peter Slattery 

NC 



Kelvin Barwick 

NC 



John Ljubenkov 

SC 



Susan Weeks 

WO 

Echinodermata 

Gordon Hendler 

Peter Slattery 

NC 



Nancy Carder 

SC 



Scott McEuen 

WO 

Miscellaneous taxa 

John Ljubenkov 

Peter Slattery 

NC 



John Ljubenkov 

SC 



Scott McEuen 

WO 

Freshwater fauna 

Rob Plotnikoff/ 

Not Applicable 

NC 


Chad Wiseman 

Not Applicable 

SC 



Jeff Cordell 

WO 


*NC: Northern California, SC: Southern California, WO: Washington & Oregon 


51 













2.5 Data management 

Data management for the West Coast stations sampled in 1999 is a component of the 
overall EMAP Western Coastal Information Management Program. The Information 
Management System is based on a centralized data storage model using standardized 
data transfer protocols (SDTP) for data exchange among program participants. The 
1999 data were submitted to the Information Manager (IM) located at the Southern 
California Coastal Water Research Project (SCCWRP) for entry into the relational 
database (Microsoft Access 2000). 

The data flow consists of interactions among four levels. Field crew leaders and 
laboratory supervisors are responsible for compiling data generated by their 
organizations and for entering the data into one or more of the SDTP tables. The State 
IM Coordinator is responsible for compiling all data generated within a state into a unified 
state database. The Western EMAP IM Coordinator (WIMC) is responsible for working 
with State Coordinators to develop the SDTP, and for creation and management of the 
centralized West Coast EMAP database. The EMAP IM Coordinator, located at the 
Atlantic Ecology Division of EPA at Narragansett, Rhode Island, is responsible for 
accepting data from Western EMAP, for placing it in the national EMAP database, and 
for transferring it to other EPA databases, such as STORET. 

Once all data tables of a particular data type (e.g., all tables containing fish data) were 
certified by the WIMC, integrated multi-state data tables were provided to the Western 
EMAP Quality Assurance Coordinator (QAC). The QAC reviewed the data with respect 
to scientific content. Necessary corrections resulting from this review process were 
returned to the Western EMAP IM Coordinator, who was responsible for working with the 
State IM Coordinator to make necessary changes. 

Following certification of all portions of the data by the QAC, the WIMC submitted the 
integrated multi-state data set to the EMAP IM Coordinator, who is the point of contact 
for data requests about the integrated data set. 

Details of the Western EMAP Information Management process are provided in Cooper 
(2000). The structure of each of the relational database tables and supporting database 
look-up tables used by the states to submit data to the WIMC are also provided in this 
document (Cooper, 2000). 

2.6 Unsamplable Area 

In Washington, 6 stations (WA99-0005, Ozette River; WA99-0028, Beardslee Slough; 
WA99-0018, Quinault River; WA99-0032, WA99-0037, Willapa Bay; WA99-0041, Grays 
River) proved to be inaccessible to sampling and were abandoned (Table 2-1). 

In Oregon, station OR99-0029 was abandoned prior to sampling because inspection 
found that it fell too far upstream and was not visited. Station QR99-0075, part of the 


52 


Tillamook Bay intensification study, was not sampled because the station was located in 
a marsh area. No sediment contaminant analyses were conducted at OR99-0044 or 
OR99-0051 because of grab failures due to large amounts of rock and shell in the 
substrate. 

In California, all stations were visited. Among the base study stations, there were no grab 
or trawl samples obtained at CA99-3019 (Carmel Bay) or CA99-3024 (San Luis Obispo 
Bay) because of rocky substrate at the sites. Site CA99-3027, located in the Ventura 
River, was not sampled because the station location was actually located on land and 
the adjacent aquatic habitat could not be sampled because it consisted of a large 
boulder substrate. Among the northern California intensification sites, no grab or trawl 
samples were obtained at stations CA99-3058 (Klamath River), CA99-3066 (Noyo 
River), CA99-3072 (Albion River), and CA99-3075 (Elk Creek) because of the presence 
of rocky substrates. No trawl was obtained at station CA99-3056 (Wilson River) 
because there was insufficient room to deploy gear. 


53 


























































3.0 Indicator Results 


3.1 Habitat Indicators 

3.1.1 Salinity 

Salinity in the bottom water for the small estuaries of West Coast states ranged from 0 
psu to 34.2 psu across the 201 stations where bottom salinities were collected. 
Approximately fifty percent of the area of the small estuaries had a salinity > 30.9 psu 
(Figure 3.1 -1). About 54% of the area of the West Coast states estuaries would be 
classified as euhaline (> 30 psu) based on the EMAP sampling. The extended left tail of 
the CDF indicates that a number of samples were taken at low salinities, but that these 
sites constituted a modest percentage of the total estuarine area. Approximately 19% of 
the area of the small estuaries had salinities less than 20 psu, while only 11% of 
estuarine area is represented by salinities less than 5 psu. The range of values for 
surface salinity was identical to that in bottom water, and the CDF of surface salinity 
values was very similar to that for bottom salinities. In interpreting these results, it is 
important to recognize that salinity can vary both tidally and seasonally, as well as with 
depth in the water column, and that these single measurements are "snapshots" during 
the sampling events. 

3.1.2 Water Temperature 

Temperature in the bottom water for the small estuaries of West Coast states ranged 
from 8.5 °C to 32.1 °C across the 201 stations where bottom temperatures were 
collected. The relatively wide range of bottom water temperature values reflects the two 
biogeographic provinces which were sampled in West Coast states. The range of 
surface water temperatures was very similar to that for bottom water temperatures (9.3 
°C to 32.1 °C). Approximately 13% of the area of the small estuaries had a temperature 
at the bottom > 20 °C, with about 19.6 % of area having bottom water temperatures < 
11.1 °C (Figure 3.1 -2). These temperatures are representative of summer conditions in 
the region. 

3.1.3 pH 

The pH of bottom waters for the small estuaries of West Coast states had the 
surprisingly wide range of from 5.1 to 10.2 across the 197 stations where bottom pH 
measurements were collected. The range for pH in surface water samples was 
identical to that for bottom waters. Approximately 91% of the area of the small estuaries 
had a pH < 8.0 (Figure 3.1 -3). Values of pH > 9 tended to be found at sites with low 
salinity (< 7 psu), with the exception of the station from Point Mugu Lagoon, California, 
where a pH of 9.3 and a salinity of 33.4 psu were recorded. Values of pH < 6.5 tended 
to be found at sites with low salinity (< 1 psu). 


55 


3.1.4 Sediment Characteristics 


The percent silt-clay of sediments ranged from 0 % to 96.4 % at the 190 stations from 
which soft sediment samples could be obtained (Figure 3.1 -4). About 65% of the area 
of the small estuaries had sediments composed of sands (< 20 % silt-clay), about 29.4 
% was composed of intermediate muddy sands (20-80 % silt-clay), and only about 5.6 
% was composed of muds (>80 % silt-clay). 

Percent total organic carbon (TOC) in sediments of small west coast estuaries ranged 
from 0 % to 7.4 % at the 190 stations from which soft sediment samples could be 
obtained (Figure 3.1 -5). About 84% of the area of the small estuaries had sediments 
with TOC levels < 1.0 %. 

3.1.5 Water Quality Parameters 

Water quality parameters are presented as water column mean values based on the 
concentration averaged over the surface, mid-water, and bottom water samples. Water 
depths during sampling ranged between 0.3 m and 30 m depth. 

Chlorophyll a 

The average water column concentration of chlorophyll a of small west coast estuaries 
(Figure 3.1 -6) ranged from 0.4 to 47.6 pg L" 1 across the 202 stations where chlorophyll 
measurements were collected. Approximately 88% of total estuarine area was 
characterized by average chlorophyll a concentrations < 7.9 pg L' 1 , while approximately 
0.6 % of estuarine area had chlorophyll a values that exceeded concentrations of 15 pg 
L 1 . There was no geographic concentration of high chlorophyll values. 

Nutrients 

The average water column concentration of nitrate + nitrite of small west coast estuaries 
(Figure 3.1 -7) ranged from 0 to 3472 pg L' 1 across the 202 stations where nitrate + 
nitrite measurements were collected. Approximately 95% of total estuarine area was 
characterized by nitrate + nitrite concentrations < 263 pg L' 1 , while approximately 2.7 % 
of estuarine area had nitrate + nitrite values that exceeded concentrations of 300 pg L' 1 . 

The average water column concentration of ammonium in small west coast estuaries 
(Figure 3.1 -8) ranged from 0 to 580 pg L' 1 across the 202 stations where ammonium 
measurements were collected. Approximately 90% of total estuarine area was 
characterized by ammonium concentrations < 125 pg L' 1 . 

The average water column concentration of total nitrogen (nitrate + nitrite + ammonium) 
in small west coast estuaries (Figure 3.1 -9) ranged from 3.2 to 3519 pg L' 1 across the 
202 stations where total nitrogen measurements were collected. Approximately 90% of 
total estuarine area was characterized by total nitrogen concentrations < 218 pg L' 1 . 


56 


The average water column orthophosphate concentration of small west coast estuaries 
(Figure 3.1 -10) ranged from 0 to 563.3 pg L' 1 across the 202 stations where 
orthophosphate measurements were collected. Approximately 95% of total estuarine 
area was characterized by orthophosphate concentrations < 158 pg L' 1 . 

The ratio of total nitrogen (nitrate + nitrite + ammonium) concentration to total 
orthophosphate concentration was calculated as an indicator of which nutrient may be 
controlling primary production in west coast small estuaries. A ratio above 16 is 
generally considered indicative of phosphorus limitation, and a ratio below 16 is 
indicative of nitrogen limitation (Geider and La Roche, 2002). The N/P ratio (Figure 3.1 
-11) ranged from 0.16 to 393.5 across the 190 stations where sufficient measurements 
were collected. Approximately 75% of estuarine area had N/P values < 16. The long 
right tail of the CDF was due to four stations representing less than 1 % of estuarine 
area with N/P ratios > 100. 

Total Suspended Solids 

The average water column concentrations of total suspended solids (TSS) in the water 
column of small west coast estuaries (Figure 3.1-12) ranged from 0 to 276.2 mg L' 1 
across the 201 stations where TSS measurements were collected. Approximately 
95% of total estuarine area was characterized by TSS concentrations < 19.1 mg L' 1 . 

Percent Light Transmission 

The percent light transmission of the water column (adjusted to a reference sample 
depth of 1 m) in small west coast estuaries (Figure 3.1 -13) ranged from 0 to 87.6% of 
surface illumination. Approximately 21.3 % of total estuarine area showed a percent 
light transmission of <10 %, and approximately 46.8 % of total estuarine area showed a 
percent light transmission of <20 %. 

3.1.6 Water Column Stratification 

As an indicator of water column stratification, two indices were calculated for the 201 
stations with temperature and salinity data. The first index was the simple difference 
between bottom and surface salinities. The second index (Ao t ) was the difference 
between the computed bottom and surface o t values, where o t is the density of a parcel 
of water with a given salinity and tmperature relative to atmospheric pressure. Results 
of the two indices were extremely similar. 

The simple stratification index ranged between -1.2 and 20.2 psu. Less than 4% of 
estuarine area showed index values < 0, indicating bottom waters less saline than 
surface waters (Figure 3.1 -14). Approximately 12% of estuarine area had index values 
> 2 psu, indicating strong stratification. The Ao t index had values ranging from -0.08 to 
+16.2. Approximately 3% of estuarine area showed Ao t index values < 0, indicating 


57 








bottom waters less saline than surface waters (Figure 3.1 -15). Approximately 12% of 
estuarine area had Ao t index values > 2, indicating strong stratification. 

The limited indication of strong water column stratification within the small west coast 
estuaries sampled is consistent with the large tidal amplitude across much of the region, 
which should lead to a high degree of water column mixing. Additionally the sampling 
period is during the summer period of low rainfall and low freshwater runoff which 
should also reduce the extent of vertical stratification during the sample period. 


Bottom Salinity 
West Coast Small Estuaries 



Figure 3.1-1. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. salinity of bottom waters. 


58 











Bottom Temperature 
West Coast Small Estuaries 



Figure 3.1-2. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. temperature of bottom waters. 


59 













Bottom pH 

West Coast Small Estuaries 



Figure 3.1-3. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. pH in bottom waters. 


60 












Percent Sediment Silt-Clay 
West Coast Small Estuaries 



Figure 3.1-4. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. percent silt-clay of sediments. 


61 












Percent Sediment Total Organic Carbon 
West Coast Small Estuaries 



Figure 3.1-5. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. percent total organic carbon of sediments. 


62 












Mean Chlorophyll a Concentration 
West Coast Small Estuaries 



Figure 3.1-6. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. water column mean concentration of chlorophyll a. 


63 









Mean Nitrate+Nitrite Nitrogen Concentration 
West Coast Small Estuaries 



0 500 1000 1500 2000 2500 3000 3500 4000 

Concentration (ug/L) 


Figure 3.1-7. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. water column mean nitrate + nitrite concentration. 


64 









Mean Ammonium Nitrogen Concentration 
West Coast Small Estuaries 



Figure 3.1-8. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. water column mean ammonium concentration. 


65 
















Mean Total Dissolved Nitrogen Concentration 
West Coast Small Estuaries 



Figure 3.1-9. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. water column mean total nitrogen (nitrate + nitrite + ammonium) concentration. 


66 










Mean Orthophosphate Phosphorus Concentration 
West Coast Small Estuaries 



Figure 3.1-10. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. water column mean orthophosphate concentration. 


67 


















Mean N:P Molar Ratio 
West Coast Small Estuaries 



0 50 100 150 200 250 300 350 400 450 

Molar Ratio 


Figure 3.1-11. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. water column mean ratio of total nitrogen (nitrate + nitrite + ammonium) 
concentration to total orthophosphate concentration. 


68 












Mean Total Suspended Solids 
West Coast Small Estuaries 



0 50 100 150 200 250 300 

Concentration (mg/L) 


Figure 3.1-12. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. water column total suspended solids concentration. 


69 














Percent Light Transmission at 1 m 
West Coast Small Estuaries 



0 10 20 30 40 50 60 70 80 90 100 

Percent Light Transmission 


Figure 3.1-13. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. percent light transmission estimated at a reference depth of 1 m in the water 
column. 


70 











Stratification Index 
West Coast Small Estuaries 



Figure 3.1-14. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. water column stratification index. 


71 





















A CT t 

West Coast Small Estuaries 



Figure 3.1-15. Percent area (and 95% C.l.) of small estuaries of the West Coast states 
vs. Ao t stratification index. 


72 
















3.2 Exposure Indicators 

3.2.1 Dissolved Oxygen 

Dissolved oxygen (DO) concentrations in the bottom water for the small estuaries of West 
Coast states ranged from 3.75 mg L' 1 to 16.3 mg L' 1 across the 200 stations where 
dissolved oxygen concentrations were measured. No observations were less than the 
value of 2 mg L' 1 considered indicative of anoxia, less than four percent of estuarine area 
had a bottom DO concentration below 5 mg L' 1 , and approximately 92% of the area of 
West Coast small estuaries had DO concentrations between 5 and 10 mg L' 1 ( Fig. 3.2-1). 
The range of dissolved oxygen (DO) concentrations in the surface waters was very similar 
to that for bottom waters (3.46 mg L' 1 to 16.3 mg L' 1 ) (Fig. 3.2-2). Approximately 83% of 
the area of West Coast small estuaries had surface DO concentrations between 5 and 10 
mg L' 1 , while nearly 11 % had DO concentrations > 10 mg/L" 1 . 

3.2.2 Sediment Contaminants 
3.2.2.1 Sediment Metals 

Concentrations of metals in sediment were measured at 190 stations, except antimony 
and silver, which were measured at only 189 stations. The mean concentration of a metal 
was calculated using all available samples with the non-detects set to 0. For comparative 
purposes, mean concentrations of metals were also calculated using the subset of 
samples in which the metals were detected (Table 3.2-1). 

Arsenic 

Arsenic was detected in 189 of the stations and had a mean concentration of 6.11 pg/g 
(Table 3.2-1). The maximum concentration of 18.6 pg/g occurred in Grays Bay in the 
Columbia River, Washington. The next two highest concentrations of 17.6 and 17.1 pg/g 
occurred in Tillamook Bay, Oregon, and the Los Angeles Harbor, respectively. Fifty 
percent of the area of the West Coast small estuaries had concentrations less than 5.53 
pg/g, and 90% of the area had concentrations less than 8.75 pg/g (Figure 3.2-3). Arsenic 
concentrations exceeded the ERL at 37 stations (14.8% of area), while no stations had 
values exceeding the ERM (Table 3.2-1). 

Cadmium 

Cadmium was detected in 164 of the stations and had a mean concentration of 0.219 
pg/g (Table 3.2-1). The maximum concentration of 4.30 pg/g occurred in the Los Angeles 
Harbor. The only other value >1 pg/g was the 2.3 pg/g concentration in Discovery Bay, 
which opens into the Strait of Juan de Fuca, Washington. Fifty percent of the area of the 
West Coast small estuaries had cadmium concentrations less than 0.15 pg/g, and 90% of 
the area had concentrations less than 0.44 pg/g (Figure 3.2-4). Cadmium concentrations 
exceeded the ERL at only 2 stations (0.1% of area), while no stations had values 
exceeding the ERM (Table 3.2-1). 


73 


Bottom Dissolved Oxygen 
West Coast Small Estuaries 



Figure 3.2-1. Percent area (and 95% C.l.) of small estuaries of the West Coast states vs. 
dissolved oxygen of bottom waters. 


74 









Surface Dissolved Oxygen 
West Coast Small Estuaries 



Figure 3.2-2. Percent area (and 95% C.l.) of small estuaries of the West Coast states vs. 
dissolved oxygen of surface waters. 


75 











Chromium 

Chromium was detected at all 190 stations and had a mean concentration of 128 (jg/g 
(Table 3.2-1). The two highest concentrations of 1770 and 1250 [jg/g both occurred in 
the Smith River, California. These were the only concentrations >1000 pg/g. Fifty 
percent of the area of the West Coast small estuaries had concentrations less than 48.6 
pg/g, and 90% of the area had concentrations less than 168 pg/g (Figure 3.2 -5). 
Chromium concentrations exceeded the ERL at 68 stations (27% of area), while 10 
stations (2.5% of area) had values exceeding the ERM (Table 3.2-1). 

Copper 

Copper was detected at all 190 stations and had a mean concentration of 26.7 pg/g 
(Table 3.2-1). The maximum concentration of 398 occurred in the Los Angeles Harbor. 
The only other value >100 pg/g was the 156 pg/g value in Santa Barbara Harbor, 
California. Fifty percent of the area of the West Coast small estuaries had concentrations 
less than 14.5 pg/g, and 90% had concentrations less than 55.2 pg/g (Figure 3.2-6). 
Copper concentrations exceeded the ERL at 54 stations (21.2% of area), while 1 stations 
(0.1% of area) had a value exceeding the ERM (Table 3.2-1). 

Lead 

Lead was detected at all 190 stations and had mean concentration of 13.6 pg/g 
(Table 3.2-1). The maximum concentration of 293 pg/g occurred in the Los Angeles 
Harbor, and the second highest value of 80 pg/g occurred in Santa Barbara Harbor, 
California. Fifty percent of the area of the small estuaries had lead concentrations less 
than 8.87 pg/g, and 90% of the area had concentrations less than 20.4 pg/g 
(Figure 3.2-7). Lead concentrations exceeded the ERL at only 5 stations (1.3% of area), 
while 1 station (0.07% of area) had a value exceeding the ERM (Table 3.2-1). 

Mercury 

Mercury was detected at 180 of the stations and had a mean concentration of 0.113 pg/g 
(Table 3.2-1). The maximum concentration of 3.11 pg/g occurred in the Estero 
Americano, California. The only other values >1 pg/g occurred in the Los Angeles Harbor 
and the Albion River, California, which had concentrations of 2.33 and 1.37 pg/g, 
respectively. Fifty percent of the area of the West Coast small estuaries had mercury 
concentrations less than 0.03 pg/g, and 90% of the area had concentrations less than 
0.16 pg/g (Figure 3.2-8). Mercury concentrations exceeded the ERL at 25 stations 
(12.1% of area), while 3 stations (0.1% of area) had values exceeding the ERM (Table 
3.2-1). 

Nickel 

Nickel was detected at all 190 stations and had a mean concentration of 47.6 pg/g (Table 
3.2-1). The two highest concentrations, 354 pg/g and 307 pg/g, both occurred in the 
Smith River, California. Fifty percent of the area of the West Coast small estuaries had 
nickel concentrations less than 18.6 pg/g, while 90% of the area had concentrations less 
than 50.0 pg/g (Figure 3.2-9). Nickel concentrations exceeded the ERL at 116 stations 
(43.7% of area), while 45 stations (9.4% of area) had values exceeding the ERM (Table 


76 


3.2- 1). Nickel concentrations in relation to the published ERM values should be 
interpreted cautiously since the ERM value has a low reliability (Long et al., 1995). 
Because of its unreliability, nickel was excluded from a recent evaluation of sediment 
quality in southern Puget Sound (Long et al., 2000). Additionally, a study of metal 
concentrations in cores on the West Coast determined an historical background 
concentration of nickel in the range of 35 - 70 ppm (Lauenstein et al., 2000), which 
brackets the value of the ERM (51.6 ppm). 

Selenium 

Selenium was detected at 78 of the stations and had a mean concentration of 0.107 pg/g 
(Table 3.2-1). The maximum concentration of 1.6 pg/g occurred in the Los Angeles 
Harbor. Of the seven other values >0.5 pg/g, six occurred in California and one in 
Oregon. Approximately 71% of the area of the West Coast small estuaries had non- 
detectable levels of selenium, and 90% had concentrations less than 0.25 pg/g (Figure 

3.2- 10). No stations exceeded either the ERL or ERM for selenium. 

Silver 

Silver was detected at 178 of the stations and had a mean concentration of 0.16 pg/g 
(Table 3.2-1). The maximum concentration of 1.13 pg/g occurred in the Los Angeles 
Harbor. The second and third highest values of 0.98 and 0.92 pg/g were found in Grays 
Bay, Washington, and San Diego Bay, respectively. Fifty percent of the area of the West 
Coast small estuaries had a silver concentrations less than 0.21 pg/g, while 90% of the 
area had concentrations less than 0.48 pg/g (Figure 3.2-11). Silver concentrations 
exceeded the ERL at only 1 station (0.1% of area) (Table 3.2-1), and no stations 
exceeded the ERM. 

Tin 

Tin was detected at 130 stations and had a mean concentration of 1.24 pg/g 
(Table 3.2-1). The maximum concentration of 17.3 pg/g occurred in the Los Angeles 
Harbor. The only other value greater than 10 pg/g was in the Albion River, California, 
which had a concentration of 11.6 pg/g. Fifty percent of the area of the West Coast small 
estuaries had a tin concentration less than 0.99 pg/g, while 90% of the area had 
concentrations less than 2.67 pg/g (Figure 3.2-12). 

Zinc 

Zinc was detected at all 190 stations and had a mean concentration of 69.5 pg/g 
(Table 3.2-1). The maximum concentration of 538 pg/g occurred in the Los Angeles 
Harbor, while the next highest value, 173 pg/g, was found in both the Santa Barbara 
Harbor and San Diego Bay. Fifty percent of the area of the West Coast small estuaries 
had zinc concentrations less than 49 pg/g, while 90% of the area had concentrations less 
than 117 pg/g (Figure 3.2-13). Zinc concentrations exceeded the ERL at 4 stations (1.2% 
of area), while 1 station (0.1% of area) had a value exceeding the ERM (Table 3.2-1). 


77 


Additional Metals 

In addition to the 11 metals discussed above, aluminum, antimony, iron, and 
manganese were measured in the sediments. The measured concentration and 
frequency of detection for each of these metals are given in Table 3.2 -1. Each of these 
four metals was detected at all of the stations, with the exception of antimony, which was 
detected at 115 stations. Not unexpectedly, aluminum and iron were the two most 
abundant metals, with mean concentrations of 44631 pg/g and 33642 pg/g, respectively. 


78 


Table 3.2-1. Summary statistics for sediment metal concentrations (|jg/g) for all stations from West Coast estuaries. The 
overall mean and the overall standard deviation (SD) were calculated using all the data, including the non-detects which 
were set to 0. (N = 190, except 189 for antimony and silver). The “mean when present” was calculated using the samples 
which had detectable concentrations of the compound. ERL and ERM values are from Long et al. (1995). 



79 


The ERL and ERM for nickel has low reliability for the West Coast. See text for discussion. 




Sediment Arsenic Concentration 
West Coast Small Estuaries 



0 5 10 15 20 


Concentration (ug/g) 


Figure 3.2-3. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of arsenic. 


80 












Sediment Cadmium Concentration 
West Coast Small Estuaries 



0 1 2 3 4 5 

Concentration (ug/g) 


Figure 3.2-4. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of cadmium. 


81 











Sediment Chromium Concentration 
West Coast Small Estuaries 



Figure 3.2-5. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of chromium. 


82 











Sediment Copper Concentration 
West Coast Small Estuaries 



0 100 200 300 400 500 


Concentration (ug/g) 


Figure 3.2-6. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of copper. 


83 










Sediment Lead Concentration 
West Coast Small Estuaries 



Figure 3.2-7. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of lead. 


84 










Sediment Total Mercury Concentration 
West Coast Small Estuaries 



Figure 3.2-8. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of mercury. 


85 











Sediment Nickel Concentration 
West Coast Small Estuaries 



Figure 3.2-9. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of nickel. 


86 









Sediment Selenium Concentration 
West Coast Small Estuaries 



Figure 3.2-10. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of selenium. 


87 










Sediment Silver Concentration 
West Coast Small Estuaries 



0 0.2 0.4 0.6 0.8 1 1.2 

Concentration (ug/g) 


Figure 3.2-11. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of silver. 


88 









Sediment Tin Concentration 
West Coast Small Estuaries 



Figure 3.2-12. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of tin. 


89 









Sediment Zinc Concentration 
West Coast Small Estuaries 



Figure 3.2-13. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of zinc. 


90 










3.2.2.2 Sediment Organics 

An overall mean concentration was calculated for sediment organics using all the 
samples (N=190) with the non-detects set to 0. “Mean concentrations when present” 
were also calculated using the subset of samples in which the compounds were detected 
(Table 3.2-2) 

Total PAHs 

PAHs were detected at 112 of the stations. One laboratory replicate from a sediment 
sample from Martin Slough in the Columbia River had individual PAH concentrations 3 to 
690 times greater than in the other three replicates from the same sample. Total PAH 
concentration for this sample was 59,878 ng/g if the high laboratory replicate was 
included, but 2427 ng/g if it was excluded. The order-of-magnitude higher concentrations 
in this replicate could be due to a drop of creosote. Because the sample appears to be an 
outlier relative to the other laboratory replicates at the station, this sample was not 
included in the total PAH analysis. 

Total PAHs had an overall mean concentration of 263 ng/g dry weight (Table 3.2-2). The 
highest concentration, 22,982 ng/g, occurred in the Los Angeles Harbor. The compounds 
2,6-Dimethylnaphthalene, 2,3,5-Trimethylnaphthalene, and 1-Methylphenanthrene 
constituted 61% of the total PAHs at the Los Angeles Harbor site. Fifty percent of the 
area of the West Coast small estuaries had a total PAH concentration less than 25 ng/g, 
and 90% of the area had a concentration less than 435 ng/g (Figure 3.2-14). On the 
average, low molecular weight (LMW) PAHs constituted 57 % of the total PAHs, while 
high molecular weight (HMW) PAHs constituted 43 % of the total PAHs (Table 3.2-2). 

Four stations exceeded the ERL for both HMW (0.2 % of area; Figure 3.2-15) and LMW 
PAHs (0.9 % of area; Figure 3.2-16), and two stations exceeded the ERL (0.2 % of area) 
for total PAHs. The ERM was exceeded only for LMW PAHs at two stations (Table 3.2- 
2 ). 

Total PCBs 

PCBs were detected at 78 of the stations, and total PCBs had an overall mean 
concentration of 3.72 ng/g dry weight (Table 3.2-2). The maximum concentration of 86.5 
ng/g dry weight occurred in San Diego Bay, while the second highest concentration of 

66.2 ng/g occurred in the Los Angeles Harbor. Seventy-three percent of the area of the 
West Coast small estuaries had non-detectable levels of PCBs, while 90% of the area 
had concentrations less than 7.5 ng/g (Figure 3.2-17). PCB18 was the most abundant 
PCB conger and made up 18% of the total PCBs on average. The next most abundant 
congener was PCB52, which made up 11% of the total PCBs. PCB18 and PCB52 were 
also the most frequently detected PCB congeners, occurring in 69 and 68 of the stations, 
respectively. The ERL for total PCBs was exceeded at 7 stations (2.2% of area), while no 
stations exceeded the ERM (Table 3.2-2). 


91 


Total DDT 

DDT or one of its metabolites was detected at 28 of the stations, including 13 in 
California, 3 in Oregon and 9 in Washington. Total DDT had an overall mean 
concentration of 3.29 and a maximum concentration of 301 ng/g dry weight in the 
Channel Island Harbor in Southern California (Table 3.2-2). The only two other values 
>50 ng/g were the 99 and 50 ng/g concentrations in the Long Beach Harbor and the Los 
Angeles Harbor, respectively. Eighty-eight percent of the area of the small estuaries had 
non-detectable levels of DDTs, while 90% of the area had total DDT concentrations less 
than 0.31 ng/g (Figure 3.2-18). The most abundant form was 4,4'-DDD, constituting 77% 
of the total DDT on average (Table 3.2-2). The concentration of 4,4'-DDD exceeded the 
ERL at 15 stations (6.1% of area), and exceeded the ERM at 3 stations (1.6% of area) 
(Table 3.2-2). The ERL for total DDT was exceeded at 17 stations (6.2% of area), while 
the ERM was exceeded at 3 stations (0.1% of area) (Table 3.2-2). 

Additional Pesticides 

Besides DDT, an additional 12 pesticides were measured in the sediments in all three 
states (Table 3.2-2). Of these Dieldrin, Endosulfan II and Mirex were never detected at 
any station. The other pesticides occurred in 3 to 11 of the 190 sediment samples. An 
overall mean concentration was calculated for each of these pesticides using all the 
samples (ISM 90) with the non-detects set to 0. Because of their low frequency of 
detection, means were also calculated for these pesticides using just the samples in 
which the pesticides were detected. Endrin had the highest concentrations, with an 
overall mean concentration of 0.36 ng/g and a mean of 7.50 ng/g at the sites where it was 
detected. All nine sites where endrin was detected had concentrations which exceeded 
the ERL but not the ERM. Trans-nonachlor was the second most abundant of the 
additional pesticides, with an overall mean of 0.21 ng/g and a mean of 5.70 ng/g where 
detected. There was an insufficient number of detects to calculate CDFs for any of the 
additional pesticides. 


92 


Table 3.2-2. Mean sediment concentrations (ng/g dry weight) and frequency of detection of the PAHs, PCBs and pesticides measured 
in all three states. The overall mean and the overall standard deviation (SD) were calculated using all the data including the non- 
detects, which were set to 0. The “mean when present” was calculated using the samples which had detectable concentrations of the 
compound. N = 190. ERL and ERM values are from Long et al. (1995). NA - not analyzed, see text. 



93 




Cumulative Percent Area 


Sediment Total PAHs 
West Coast Small Estuaries 



Figure 3.2-14. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of total PAHs. 


94 











Cumulative Percent Area 


Sediment High Molecular Weight PAHs 
West Coast Small Estuaries 



Figure 3.2-15. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of high molecular weight PAHs. 


95 













Sediment Low Molecular Weight PAHs 
West Coast Small Estuaries 


100 


TO 

3 

E 

3 

o 




S 80 


c 

0 ) 

§ 60 

Q. 

0) 

> 


3 40 


20 


0 


0 


• Cumulative Percent 


- - - - ■ 95% Confidence Interval 


5000 


10000 15000 

Concentration (ng/g) 


20000 


25000 


Figure 3.2-16. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of low molecular weight PAHs. 


96 









Sediment Total PCBs 
West Coast Small Estuaries 



0 10 20 30 40 50 60 70 80 90 100 


Concentration (ng/g) 


Figure 3.2-17. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of total PCBs. 


97 













Sediment Total DDT Concentration 
West Coast Small Estuaries 



0 50 100 150 200 250 300 350 


Concentration (ng/g) 


Figure 3.2-18. Percent area (and 95% C.l.) of West Coast small estuaries vs. sediment 
concentration of total DDT. 


98 









3.2.3 Sediment Toxicity 

3.2.3.1 Ampelisca abdita 

Sediment toxicity tests with the amphipod Ampelisca abdita were conducted on a total of 
190 sediment samples, 41 in Washington, 76 in Oregon, and 73 in California. Control 
conditions for a successful toxicity test with this species require a mean of 90% survival in 
the five replicates in control sediments, with no replicate less than 80%. If the amphipods 
do not survive at acceptable levels in control replicates, it may be possible that they were 
unduly stressed due to shipping or laboratory holding conditions and that their response 
to test sediments may be compromised. The quality control requirements were not met in 
24 of the 190 samples, and these samples were excluded from the CDF analysis, leaving 
166 samples for analysis. The stations that were excluded included 7 in Washington, 6 in 
Oregon and 11 in California. 

The control-corrected survivorship of Ampelisca abdita in bioassays of sediments 
collected in West Coast small estuaries (Figure 3.2 -19) ranged from 0 % to 109.9 % 
across the 166 stations that were included in the analysis. Approximately 9.2 % of the 
area of West Coast small estuaries (represented by 12 sites) had control-corrected 
survivorship of Ampelisca abdita in sediment bioassays < 80%. Over 19 % of area had 
control-corrected survivorship > 100 %, indicating better survival of amphipods in test 
sediments than in controls. 

Four stations in Washington, one in Oregon and seven stations in California had mean 
survival in test sediments less than 80%. Only four stations had mean survival in test 
sediments less than 60%; these included two sites in the Smith River, one site in the Los 
Angeles River in California, and one site in Grays Bay, Washington. Of the 12 sites with 
survival less than 80%, five sites showed evidence of high levels of sediment 
contaminants. 

3.2.3.2 Arbacia punctulata 

Sediment porewater toxicity tests with sea urchins, Arbacia punctulata, were conducted 
on 41 sites in Washington, 36 base stations in Oregon, and 47 base stations in California, 
for a total of 124 samples. No sediments from the intensification sites in northern 
California or Tillamook Bay, Oregon, were tested with Arbacia. Five test sediments from 
Oregon (OR99-0018,..20,..24,..25,..26) and thirteen from California (CA99- 
0014,..15,..16,..17,..20, ..21,..22,..23,..25,..26,..28,..29,..30) arrived at the testing 
laboratory at temperatures that exceeded the acceptable temperature criterion. Since it is 
not known what effect the elevated temperatures may have on porewater toxicity, test 
results from those sediment samples were excluded from the CDF analysis. As 
described in Section 2.4.2.2.2, the designation of toxicity for Arbacia bioassays utilized 
two statistical test criteria for individual samples, rather than using a single survival 
standard as was done with the Ampelisca bioassays. The statistical test criteria in 
practice translate to a control corrected standard of approximately 85% fertilization 
success or embryonic survival in the CDF based analysis of data. 


99 


The control corrected mean percent fertilization of A. punctulata eggs in the 100% of the 
water quality adjusted (WQA) porewater treatment ranged from 0.2 % to 106 %, across 
the 97 stations that were included in the analysis (Figure 3.2-20). Approximately 7.4 % of 
the area of the West Coast small estuaries (12 sites) had control corrected mean percent 
fertilization of < 86 %, and thus would be considered to have toxic sediments based on 
this bioassay. For the 50 % of WQA porewater treatment, the range of mean percent 
fertilization was 5 % to 106 %, while 2.3% of estuarine area (6 sites) had values < 86% 
fertilization (Figure 3.2-21). For the 25 % of WQA porewater treatment, the range of 
mean percent fertilization was 50 % to 106 %, while 0.8 % of estuarine area (4 sites) had 
values < 85% fertilization (Figure 3.2-22). 

The control corrected mean percent successful development of A. punctulata embryos in 
the 100 % of WQA porewater treatment ranged from 0 % to 103 %, across the 97 stations 
that were included in the analysis (Figure 3.2-23). Approximately 45 % of the area of the 
West Coast small estuaries (52 sites) had control corrected mean percent embryo 
development success of < 87 %, and thus would be considered to have toxic sediments 
based on this bioassay. For the 50 % of WQA porewater treatment, the range of mean 
percent embryo development success was 0 % to 103 %, while 19.7 % of estuarine area 
(27 sites) had values < 85 % embryo development success (Figure 3.2-24). For the 25 % 
of WQA porewater treatment, the range of mean percent embryo development success 
was 0 % to 103 %, while 2.5 % of estuarine area (6 sites) had values < 86 % embryo 
development success (Figure 3.2-25). 


100 


Sediment Toxicity 
West Coast Small Estuaries 



Figure 3.2-19. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
control-corrected survivorship of Ampelisca abdita. 


101 










Percent Egg Fertilization Success 
of Arbacia punctulata - 100% of 
Water Quality Adjusted Porewater 
West Coast Small Estuaries 



Percent Egg Fertilization Success (%) 


Figure 3.2-20. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
fertilization of Arbacia punctulata eggs for the 100% water quality adjusted 
porewater concentration. 


102 













Percent Egg Fertilization Success 
of Arbacia punctulata - 50% of 
Water Quality Adjusted Porewater 
West Coast Small Estuaries 



Percent Egg Fertilization Success (%) 


Figure 3.2-21. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
fertilization of Arbacia punctulata eggs for the 50% water quality adjusted 
porewater concentration. 


103 









Percent Egg Fertilization Success 
of Arbacia punctulata - 25% of 
Water Quality Adjusted Porewater 
West Coast Small Estuaries 



0 20 40 60 80 100 120 

Percent Egg Fertilization Success (%) 


Figure 3.2-22. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
fertilization of Arbacia punctulata eggs for the 25% water quality adjusted 
porewater concentration. 


104 










Percent Embryonic Development Success 
of Arbacia punctulata - 100% of 
Water Quality Adjusted Porewater 
West Coast Small Estuaries 



Percent Embryonic Development Success (%) 


Figure 3.2-23. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 
successful embryonic development of Arbacia punctulata for the 100% water 
quality adjusted porewater concentration. 


105 













Percent Embryonic Development Success 
of Arbacia punctulata - 50% of 
Water Quality Adjusted Porewater 
West Coast Small Estuaries 



Percent Embryonic Development Success (%) 


Figure 3.2-24. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 

successful embryonic development of Arbacia punctulata for the 50% water quality 
adjusted porewater concentration. 


106 














Percent Embryonic Development Success 
of Arbacia punctulata - 25% of 
Water Quality Adjusted Porewater 
West Coast Small Estuaries 



0 20 40 60 80 100 120 

Percent Embryonic Development Success (%) 


Figure 3.2-25. Percent area (and 95% C.l.) of West Coast small estuaries vs. percent 

successful embryonic development of Arbacia punctulata for the 25% water quality 
adjusted porewater concentration. 


107 











3.2.4 Tissue Contaminants 


Residues of a suite of metals, PCBs, and pesticides were measured in the whole bodies 
of fish (see Table 2-5 for list of compounds). Flatfish (pleuronectiformes) were the 
designated target species, while various perch-like species (perciformes) were the 
secondary target group when flatfish were not captured. If neither flatfish nor perch-like 
species were present, whatever abundant species was captured at the site was utilized 
as an “other” group. Twelve of the fifteen sites with residues measured on the “other” 
species occurred in the Northern California intensive sites. The specific fish species in 
each group and their relative abundance are given in Table 3.2-3. Combined across all 
three states, fish residues were measured at 145 to 152 sites, depending upon the 
analyte, with flatfish measured at 112 to 119 of these sites (Tables 3.2 -4 and 3.2 -5). 
Because it is not clear that the sites without any fish captured for residue analysis were 
distributed randomly, and due to the uncertainties associated with mixing different guilds 
of fish species, the fish residue data are presented as summary statistics rather than as 
CDFs to estimate areas. 

Fish tissue residues of the 11 metals measured in all three states are summarized for all 
fish species combined and for each fish group in Table 3.2 -4. Aluminum, with an 
average concentration of 122 pg/g for all fish species, had a residue about seven-times 
greater than zinc, the metal with the second highest concentration. Silver, mercury, 
cadmium, and lead had the lowest residues, with all four having a mean concentration 
<0.1 pg/g when averaged for all species. The concentrations of the various metals were 
generally similar among the three fish groups. The greatest difference was with nickel, 
which had mean values of 0.38 pg/g and 0.11 pg/g in the flatfish and perches, 
respectively, compared to an average of 2.07 pg/g in the “other” group. Though the mean 
values were similar, the sample site location of the maximum tissue residues varied for 
each of the metals. For example, all the mercury residues >0.05 pg/g occurred in 
California, and the two residues >0.1 pg/g occurred in San Diego Bay and in the Albion 
River in Northern California. In comparison, the two highest arsenic concentrations 
occurred in Discovery Bay, Washington; the highest lead value occurred in Willapa Bay, 
Washington; and the highest copper residues occurred in Tillamook Bay, Oregon. 

Fish tissue residues of total PCBs, total DDT, and other pesticides are summarized in 
Table 3.2 -5. Total DDT had the highest residue of all the neutral organic contaminants, 
averaging about 44.7 ng/g when averaged over all the fish species. 4,4'-DDE constituted 
83% to 91% of the total DDT in all three fish groups. In contrast to the metals, total DDT 
showed a considerable difference among the fish groups, ranging from 1.92 ng/g in the 
“other” group to 245 ng/g in the perciform species. Total PCBs had the second highest 
residue of the neutral organics, averaging about 17 ng/g for all fish species combined. 
PCB138 and PCB153 were the two most abundant PCB congeners, making up 34% to 
60% of the total PCBs in the three fish groups. As with total DDT, total PCBs showed a 
considerable difference among the fish groups, ranging from about 1 ng/g in the “other” 
group to 83 ng/g in the perciform species. It is possible that these differences among fish 
groups are largely a result of where the different types of fish species were collected 
rather than an inherent difference in bioaccumulation by the fish groups. Genyonemus 


108 


lineatus (white croaker) was the most abundant species in the perciform group, and all 
the white croaker used for fish residues were obtained from either the Los Angeles 
Harbor or the Long Beach Harbor. These two industrialized harbors were the sites for 
the maximum fish residues for both total PCBs and total DDT and had relatively high total 
PCB and total DDT sediment concentrations. In comparison, most of the individuals 
making up the “other” group were captured in the non-industrialized, small, Northern 
California estuaries. 

The residues of the thirteen additional pesticides were considerably lower than that of 
total DDT (Table 3.2 -5). Endosulfan sulfate had the highest residue of the other 
pesticides, with a concentration of 1.24 ng/g when averaged over all the fish species. No 
other pesticide was >1 ng/g when averaged over all the fish species, though Trans- 
nonachlor averaged 3.08 ng/g in the perciform species. Mirex and Toxaphene were 
never detected in any fish. The three fish groups showed several differences in the mean 
residues of these pesticides. None of the thirteen additional pesticides were detected in 
the “other” fish group. The primary differences between the flatfish and perch-like species 
were the absence of detectable levels of Endosulfan sulfate and the higher residues of 
Trans-nonachlor in the perch-like species. As mentioned above, differences in where the 
various species groups were collected may have contributed to these among-group 
differences in residue patterns. 

Tissue residues of certain organic pollutants (e.g., DDT and PCBs) and organometals 
(e.g., mercury) tend to increase in larger organisms. It is not possible to directly evaluate 
this effect using the EMAP data because different size fish were composited into single 
analytical samples. It is possible, however, to assess whether there is any relationship 
between the average size of the individuals in a composite and the composite residue. 
Using mercury as the test compound, a significant positive linear relationship was 
observed between average wet weight of the individuals and mercury 
concentration when all fish species were combined as well as with Pleuronectes vetulus. 
These preliminary results suggest that residues for the organic pollutants and 
organometals would tend to be higher in larger fish in the small estuaries of the Pacific 
Coast. 


109 


Table 3.2-3. The species composition and relative abundance of the three fish groups 
used in the tissue residue analysis. The percent within a group is the relative abundance 
of the species within the group in which it is included. The overall percent is the relative 
abundance of the species when all the fish species are combined. 


Fish Group 

Number 

Percent within 
Group 

Overall Percent 

Pleuronectiformes 

Pleuronectes vetulus 

47 

37.0 

29.4 

Platichthys stellatus 

43 

33.9 

26.9 

Citharichthys stigmaeus 

21 

16.5 

13.1 

Paralichthys californicus 

10 

7.87 

6.25 

Psettichthys melanostictus 

3 

2.36 

1.88 

Citharichthys sordidus 

1 

0.79 

0.63 

Pleuronectes isolepis 

1 

0.79 

0.63 

Symphurus atricauda 

1 

0.79 

0.63 

Perciformes 

Genyonemus lineatus 

6 

33.3 

3.75 

Cymatogaster aggregata 

5 

27.8 

3.13 

Paralabrax nebulifer 

3 

16.7 

1.88 

Gasterosteus aculeatus 

2 

11.1 

1.25 

Embiotoca lateralis 

1 

5.56 

0.63 

Paralabrax maculatofasciatus 

1 

5.56 

0.63 

“Other” 

Leptocottus armatus 

12 

80.0 

7.50 

Oligocottus rimensis 

2 

13.3 

1.25 

Atherinops affinis 

1 

6.67 

0.63 


110 







Table 3.2-4. Fish tissue residues of metals measured in all three states. The “All Fish” 
group is the overall average combining all species. The species compositions of the 
pleuronectiform, perciform, and “other” groups are given in Table 3.2 -3. 


Metal 

Mean 
(ucj/q wet) 

SD 

Minimum 

Maximum 

Number 

Samples 

All Fish 

Aluminum 

122 

110 

3.36 

569 

145 

Arsenic 

0.60 

0.63 

0.00 

3.77 

146 

Cadmium 

0.03 

0.04 

0.00 

0.31 

145 

Chromium 

1.11 

3.48 

0.07 

36.5 

145 

Copper 

1.25 

1.04 

0.00 

7.77 

145 

Lead 

0.06 

0.10 

0.00 

0.84 

145 

Mercury 

0.02 

0.02 

0.00 

0.11 

149 

Nickel 

0.52 

1.74 

0.00 

15.1 

145 

Selenium 

0.37 

0.14 

0.00 

0.83 

147 

Silver 

0.01 

0.02 

0.00 

0.27 

145 

Zinc 

17.7 

7.09 

7.84 

39.1 

145 

Pleuronectiformes 

Aluminum 

116 

110 

3.36 

568 

112 

Arsenic 

0.61 

0.70 

0 

3.77 

113 

Cadmium 

0.03 

0.05 

0 

0.31 

112 

Chromium 

1.00 

3.47 

0.07 

36.5 

112 

Copper 

1.21 

1.12 

0 

7.77 

112 

Lead 

0.05 

0.10 

0 

0.84 

112 

Mercury 

0.02 

0.02 

0 

0.09 

116 

Nickel 

0.38 

1.30 

0 

13.2 

112 

Selenium 

0.35 

0.13 

0 

0.63 

114 

Silver 

0.01 

0.03 

0 

0.27 

112 

Zinc 

18.8 

6.95 

7.9 

39.1 

112 

Perciformes 

Aluminum 

117 

82.2 

15.2 

266 

18 

Arsenic 

0.76 

0.29 

0.30 

1.27 

18 

Cadmium 

0.01 

0.01 

0.00 

0.04 

18 

Chromium 

0.46 

0.59 

0.12 

2.66 

18 

Copper 

1.30 

0.86 

0.68 

4.44 

18 

Lead 

0.10 

0.10 

0.00 

0.37 

18 

Mercury 

0.05 

0.02 

0.01 

0.11 

18 

Nickel 

0.11 

0.16 

0.00 

0.53 

18 

Selenium 

0.52 

0.17 

0.17 

0.83 

18 

Silver 

0.01 

0.01 

0.00 

0.04 

18 

Zinc 

15.06 

7.56 

7.84 

37.0 

18 

“Other” 

Aluminum 

174 

127 

46.1 

485 

15 

Arsenic 

0.33 

0.08 

0.23 

0.50 

15 

Cadmium 

0.01 

0.01 

0.00 

0.03 

15 


Ill 


Table continued on next page 











Chromium 

2.73 

5.02 

0.27 

19.8 

15 

Copper 

1.51 

0.42 

1.01 

2.39 

15 

Lead 

0.06 

0.05 

0.00 

0.17 

15 

Mercury 

0.03 

0.02 

0.00 

0.10 

15 

Nickel 

2.07 

3.84 

0.06 

15.1 

15 

Selenium 

0.39 

0.09 

0.22 

0.56 

15 

Silver 

0.01 

0.00 

0.00 

0.01 

15 

Zinc 

13.0 

4.73 

9.46 

29.0 

15 


112 





Table 3.2-5. Fish tissue residues of total PCBs, total DDT and the additional pesticides 
measured in all three states. The “All Fish” group is the overall average combining all 
species. The species composition of the pleuronectiform, perciform, and “other” groups 
are given in Table 3.2 -3. 


Compound 

Mean 
(nq/q wet) 

SD 

Minimum 

Maximum 

Number 

Samples 

All Fish 

Total PCBs 

17 

47.9 

0.00 

331 

152 

Aldrin 

0.04 

0.28 

0.00 

2.40 

149 

Alpha-chlordane 

0.18 

1.07 

0.00 

11.5 

149 

Total DDT 

44.7 

219 

0.00 

2509 

148 

Dieldrin 

0.05 

0.24 

0.00 

1.40 

149 

Endosulfan Sulfate 

1.24 

3.34 

0.00 

21.4 

151 

Endosulfan 1 

0.10 

0.63 

0.00 

5.17 

150 

Endosulfan II 

0.05 

0.26 

0.00 

2.09 

149 

Endrin 

0.10 

0.43 

0.00 

3.81 

149 

Heptachlor 

0.45 

1.44 

0.00 

9.80 

149 

Heptachlor Epoxide 

0.02 

0.16 

0.00 

1.26 

149 

Lindane (gamma-BHC) 

0.01 

0.13 

0.00 

1.62 

149 

Mi rex 

0.00 

0.00 

0.00 

0.00 

149 

Trans-nonachlor 

0.58 

2.60 

0.00 

27.1 

149 

Toxaphene 

0.00 

0.00 

0.00 

0.00 

149 

Pleuronectiformes 

Total PCBs 

8.89 

21.5 

0 

133 

119 

Aldrin 

0.05 

0.32 

0 

2.40 

116 

Alpha-chlordane 

0.08 

0.38 

0 

3.55 

116 

Total DDT 

19.0 

45.9 

0 

311 

115 

Dieldrin 

0.07 

0.27 

0 

1.40 

116 

Endosulfan Sulfate 

1.59 

3.71 

0 

21.4 

118 

Endosulfan 1 

0.13 

0.71 

0 

5.17 

117 

Endosulfan II 

0.05 

0.26 

0 

2.09 

116 

Endrin 

0.12 

0.48 

0 

3.81 

116 

Heptachlor 

0.58 

1.61 

0 

9.80 

116 

Heptachlor Epoxide 

0.02 

0.14 

0 

1.16 

116 

Lindane (gamma-BHC) 

0.01 

0.15 

0 

1.62 

116 

Mi rex 

0.00 

0.00 

0 

0.00 

116 

Trans-nonachlor 

0.26 

0.76 

0 

4.57 

116 

Toxaphene 

0.00 

0.00 

0 

0.00 

116 

Perciformes 

Total PCBs 

83.5 

109 

0.00 

331 

18 

Aldrin 

0.00 

0.00 

0.00 

0.00 

18 

Alpha-chlordane 

0.98 

2.88 

0.00 

11.50 

18 

Total DDT 

245 

593 

0.00 

2509 

18 

Dieldrin 

0.00 

0.00 

0.00 

0.00 

18 

Endosulfan Sulfate 

0.00 

0.00 

0.00 

0.00 

18 


113 

Table continued on next page 









Endosulfan 1 

0.00 

0.00 

0.00 

0.00 

18 

Endosulfan II 

0.08 

0.36 

0.00 

1.51 

18 

Endrin 

0.06 

0.24 

0.00 

1.01 

18 

Heptachlor 

0.00 

0.00 

0.00 

0.00 

18 

Heptachlor Epoxide 

0.07 

0.30 

0.00 

1.26 

18 

Lindane (gamma-BHC) 

0.00 

0.00 

0.00 

0.00 

18 

Mi rex 

0.00 

0.00 

0.00 

0.00 

18 

Trans-nonachlor 

3.08 

6.87 

0.00 

27.1 

18 

Toxaphene 

“Other” 

0.00 

0.00 

0.00 

0.00 

18 

Total PCBs 

1.08 

1.89 

0.00 

4.70 

15 

Aldrin 

0.00 

0.00 

0.00 

0.00 

15 

Alpha-chlordane 

0.00 

0.00 

0.00 

0.00 

15 

Total DDT 

1.92 

3.22 

0.00 

9.00 

15 

Dieldrin 

0.00 

0.00 

0.00 

0.00 

15 

Endosulfan Sulfate 

0.00 

0.00 

0.00 

0.00 

15 

Endosulfan 1 

0.00 

0.00 

0.00 

0.00 

15 

Endosulfan II 

0.00 

0.00 

0.00 

0.00 

15 

Endrin 

0.00 

0.00 

0.00 

0.00 

15 

Heptachlor 

0.00 

0.00 

0.00 

0.00 

15 

Heptachlor Epoxide 

0.00 

0.00 

0.00 

0.00 

15 

Lindane (gamma-BHC) 

0.00 

0.00 

0.00 

0.00 

15 

Mi rex 

0.00 

0.00 

0.00 

0.00 

15 

Trans-nonachlor 

0.00 

0.00 

0.00 

0.00 

15 

Toxaphene 

0.00 

0.00 

0.00 

0.00 

15 


114 






3.3 Biotic Condition Indicators 

A total of 187 0.1 -m 2 benthic samples (grabs or combined cores) were collected in the 
three states: 47 in the base stations in California, 25 in the intensive stations in Northern 
California, 49 in the base stations in Oregon, 29 in the intensive stations in Tillamook, 
Oregon, and 37 in the base stations in Washington. Average penetration of the 187 
samples was 10.3 cm, although five grabs and six core samples had a penetration less 
than 5 cm. These eleven samples had an average benthic density about one-third 
greater than the three-state average and so were included in the analysis. 

3.3.1 Infaunal Species Richness and Diversity 

A total of 841 benthic taxa, plus an additional 26 colonial species growing on hard 
substrates (e.g., bryozoans on shell hash), were found in the 187 benthic samples. Due 
to difficulties in standardizing the count of colonial species, such species were excluded 
from the estimates of abundance and the count of number of species per sample. Insects 
were included as a single taxon in the current analyses. Species richness averaged 22.2 
species per sample (0.1 -m 2 ) in the three states, while average species richness among 
the states ranged from a low of 14.3 species per sample in Oregon to a high of 28.6 in 
California (Table 3.3-1). The Northern California intensive sites tended to have a lower 
species richness, and without inclusion of these sites, the species richness increased in 
the base California sites to an average of 38.2 species per sample. Across the three 
states, species richness ranged from 1 to 157 species per grab (0.1-m 2 ). Of the five 
benthic samples that only had one species, two occurred in California, two in Oregon, and 
one in Washington. Four of these stations with low species richness occurred at stations 
with bottom salinities <1 psu, while the fifth occurred at a station with a bottom salinity of 
13.9 psu. Of the three stations with >100 species per sample, two occurred in Discovery 
Bay and the other in Freshwater Bay, both in the Strait of Juan de Fuca, Washington. All 
these stations with high species richness had bottom salinities >30 psu. 

On an areal basis, approximately 50% of the area of the West Coast small estuaries had 
a species richness of < 17 species per sample, and 90% of the area had a species 
richness less than 62 species per sample (Figure 3.3-1). Because of the small area of 
the Northern California estuaries compared to rest of the coast, exclusion of the Northern 
California intensive sites had an inconsequential effect on these areal estimates. 

The diversity index FI' (log base 2 derived) averaged 2.33 in the three states and ranged 
from 0 to 5.93 (Table 3.3-1). Across the states, average FT ranged from a low of 1.88 in 
Oregon to a high of 2.68 in California. FI' tended to be lower in small Northern California 
estuaries, and for comparison, the exclusion of these intensive sites increased the 
average for the California base station to 3.33. The stations with an FI' of 0 were the five 
stations with a single species per sample mentioned above. The maximum FI' (5.93) 
occurred in the Discovery Bay, Washington, sample that contained 147 species. 


115 


On an areal basis, 50% of the area of the West Coast small estuaries had an H' less than 
2.80, and 90% of the area had an H' less than 4.18 (Figure 3.2 -2). As with species 
richness, exclusion of the Northern California stations had almost no effect on these areal 
estimates. 

3.3.2 Infaunal Abundance and Taxonomic Composition 

Benthic density averaged 1378.9 individuals per sample in the three states and ranged 
from 1 to 41,582 individuals per sample (Table 3.3-1). Average density across the states 
ranged from a low of 482.5 individuals per sample in Washington to a high of 2620.7 
individuals per sample in California (Table 3.3-1). Benthic density in the Northern 
California intensive sites tended to be higher than the rest of the state, and if these small 
estuarine systems are excluded, benthic density averaged 1033.0 individuals per sample 
in the base stations in California (Table 3.3-1). Across the three states, six stations had 
densities <10 individuals/sample. Three of these low-density stations occurred at sites 
with a salinity <0.5 psu, while the other three occurred at sites with salinities ranging from 
about 1 to 9 psu. The two stations with the greatest benthic densities, 41,582 and 32,285 
individuals per sample, both occurred in the Smith River in Northern California. The only 
other station with >20,000 individuals/sample occurred in the Little River, also in Northern 
California. The amphipods Americorophium spinicorne and A. salmonis constituted 
between 89% and 98% of the individuals at these stations. Salinity at these Smith River 
stations was 8-10 psu, while salinity at the Little River station was 31.2 psu. 

On an areal basis, 50% of the area of the West Coast small estuaries had a benthic 
density less than 151 individuals/sample, and 90% of the area had a density less than 
1157 individuals/sample (Figure 3.3-3). As with species richness and H' diversity, 
exclusion of the Northern California stations had an inconsequential effect on the these 
areal estimates. 

The abundance, taxonomic grouping, and classification of the 10 most abundant benthic 
species from the three states are given in Table 3.3-2. These ten numerically dominant 
species made up 75% of the total fauna. The amphipods Americorophium spinicorne and 
A. salmonis were the two most abundant species, making up 54% of the total fauna. 
Oligochaetes were the third most abundant taxon, making up 7% of the total fauna, as 
well as being the most frequently captured taxon. Of the remaining seven numerically 
abundant species, six were polychaetes and one was an amphipod. The maximum 
abundances of six of the numerically dominant species, including all three amphipod 
species, occurred in the small estuaries of Northern California. With their high densities 
and small area, the Northern California intensive sites have a disproportionate impact on 
the three-state summary statistics. Therefore, the summary statistics for the three states 
are also presented for the 10 most abundant benthic species excluding the Northern 
California intensive sites (Table 3.3-3). Americorophium spinicorne and A. salmonis were 
still the two most abundant species in the three states, although their densities were only 
about 15% to 30% of their values when Northern California was included. Another 
difference when the Northern California stations are excluded is that the polychaete 
Owenia fusiformis and the amphipod Grandidierella japonica were included among the 
numerically dominant species while Neanthes and Eogammarus drop out. 

Tables 3.3-2 and 3.3-3 list the classification of the numerically dominant species as 
native, nonindigenous, cryptogenic, or indeterminate. Cryptogenic species are species of 
uncertain geographic origin (Carlton, 1996), while indeterminate taxa are those taxa not 
identified to a sufficiently low level to classify as native, nonindigenous, or cryptogenic 
(Lee et al., 2003). Of the 10 numerically dominant species (Table 3.3-2), five were native, 
two were indeterminate, two were nonindigenous, and one was classified as cryptogenic. 


116 


These three nonindigenous and cryptogenic species constituted less than 6% of the total 
benthic abundance. When the Northern California sites are excluded, the ten numerically 
dominant species in the three states are composed of three natives, two indeterminate 
taxa, three nonindigenous species, and two cryptogenic species (Table 3.3-3). The 
relative abundance of the combined, numerically dominant nonindigenous and 
cryptogenic species was 15.3% (Table 3.3-3) when the Northern California sites were 
excluded. This contribution to total abundance was more than twice the relative 
abundance (5.7%, Table 3.3-2) calculated when the Northern California sites were 
included. 


117 


Benthic Species Richness 
West Coast Small Estuaries 



Number of Species 


Figure 3.3-1. Percent area (and 95% C.l.) of West Coast small estuaries vs. benthic 
infaunal species richness. 


118 









Shannon-Weiner Diversity Index 
West Coast Small Estuaries 



Figure 3.3-2. Percent area (and 95% C.l.) of West Coast small estuaries vs. benthic 
infaunal FT diversity. 


119 









Cumulative Percent Area 


Total Number of Benthic Organisms 
West Coast Small Estuaries 



0 5000 10000 15000 20000 25000 30000 35000 40000 45000 

Number of Organisms 


Figure 3.3-3. Percent area (and 95% C.l.) of West Coast small estuaries vs. benthic 
infaunal total abundance. 


120 













121 




Table 3.3-2. Abundance, taxonomic grouping, and classification of the ten most abundant benthic species in the three 
states including the intensification sites in Northern California and Tillamook, Oregon (N=187). * = maximum value 
occurred in the Northern California intensification sites. Taxonomic groupings: A = amphipod, O = oligochaete, P = 
polychaete. Classification of the species: Native, NIS = nonindigenous, Crypto. = cryptogenic, Indeter. = indeterminate 
taxa (see text for definitions). 



122 




Table 3.3-3. Abundance, taxonomic grouping, and classification of the ten most abundant benthic species in the three 
states excluding the Northern California intensification stations (N=162). Taxonomic groupings: A = amphipod, O = 
oligochaete, P = polychaete. Classification of the species: Native, NIS = nonindigenous, Crypto. = cryptogenic, Indeter. 
indeterminate taxa (see text for definitions). 



123 





3.3.3 Demersal Species Richness and Abundance 

To measure abundance and composition, fish were sampled with 16-foot bottom otter 
trawls in all three states. There was a total of 144 successful trawls of at least 5 minute 
duration across the three states, with 37 in the base stations in California, 2 in the 
intensive stations in Northern California, 43 in the base stations in Oregon, 28 in the 
intensive stations in Tillamook, Oregon, and 34 in Washington. Trawls were pulled at an 
average speed of 1.7 knots for an average duration of 9.9 minutes (Table 3.3-4). Due to 
the number of stations without successful trawls, the analysis of the fish trawl data is 
limited to summary statistics and species composition, and no CDFs are presented. 

Table 3.3-5 shows the mean number of individuals and species captured per trawl for the 
three states combined and in each of the individual states. The number of individuals per 
trawl averaged 33.7 fish per trawl, with a low of 13.9 in Oregon and a high of 68.0 in 
California. Species richness averaged 3.53 fish species per trawl, with a low of 2.63 in 
Oregon and a high of 5.46 in California. A total of 77 fish species were identified from the 
base stations in the three states, and no additional fish species were collected from the 
additional trawls in the small Northern California estuaries and Tillamook Bay. However, 
two additional species, Oligocottus maculosus and Salmo clarkii, were captured in beach 
seines at a station in Washington that was too shallow to pull the otter trawl. The results 
from these seines are not included in the summary statistics. 

The 10 most abundant fish species across the entire coast are given in Table 3.3-6. 
These 10 numerically dominant species constituted 81% of the total fauna. Pleuronectes 
vetulus, the English sole, was both the most abundant and frequently collected species 
along the West Coast. Citharichthys stigmaeus, the speckled sanddab, was the second 
most abundant fish. These two flatfish made up more than 50% of the individuals 
captured in the three states and were among the top five most abundant species in all 
three states (Table 3.3-7). Oregon and Washington had similar species composition and 
shared four of the five numerically dominant species (Table 3.3-7). Two of the abundant 
species in California, Genyonemus lineatus and Seriphus politus, were not found in the 
other states. 


124 


Table 3.3-4. Trawl duration and speed averaged across California, Oregon, and Washington (N=141) and in each individual 
state. SD = standard deviation. Durations are given in minutes and fractions of minutes. Trawls with durations less than 5 
minutes were not use in the analysis and are not included in the table. 



125 




Table 3.3-5. Mean number of fish captured per trawl and mean number of fish species per trawl averaged across 
California, Oregon, and Washington (N=144) and for each individual state. SD = standard deviation. 



126 




Table 3.3-6. Ten numerically dominant fish species averaged across California, Oregon, and Washington, including both 
the base and intensive stations (ISM 44). Relative abundance is the percentage the species makes up of the total 
abundance. Frequency is the number (or percent) of trawls in which each species was captured in the three states. 



127 





128 




4.0 References 

American Society for Testing and Materials (ASTM). 1991. Guide for conducting 10-day 
static sediment toxicity tests with marine and estuarine amphipods. ASTM 
Standard Methods Volume 11.04, Method Number E-1367-90. ASTM, 

Philadelphia, PA. 

Bourgeois, P.E., V.J. Sclafani, J.K. Summers, S. C. Robb, and B.A.Vairin. 1998. Think 
before you sample. GEOWorld. Vol. 11: No 12. 

Carlton, J. T. 1996. Biological invasions and cryptogenic species. Ecology 77:1653-1654. 

Carlton, J.T. and J.B. Geller. 1993. Ecological roulette: the global transport of 
nonindigenous marine organisms. Science 261:78-82. 

Cohen, A. and Carlton, J.T. 1995. Nonindigenous aquatic species in a United States 
estuary: A case study of the biological invasions of the San Francisco Bay and 
Delta. Report for the National Sea Grant College Program, DT and the U.S. Fish 
and Wildlife Service, Washington, D.C. Report No. PB 96-166525. 

Cooper, S.R. and G.S. Brush. 1991. Long-term history of Chesapeake Bay anoxia. 
Science 254:993-996. 

Cooper, L. 2000. West EMAP Revised Information Management Plan for 2000. Draft. 14 
p. plus Appendices A-D. 

Copping, A. and B.C. Bryant. 1993. Pacific Northwest Regional Marine Research 

Program, Vol. 1. Research Plan, 1992-1996. Office of Marine Environmental and 
Resource Programs, University of Washington, Seattle. 

Culliton, T.J., M.A. Warren, T.R. Goodspeed, D.G. Remeer, C.M. Blackwell, and 

J.J. McDonough, III. 1990. 50 Years of Population Change along the Nation’s 
Coasts, 1960-2010. NOAA, Office of Oceanography and Marine Assessment, 
National Ocean Service, Coastal Trends Series, Rockville, MD. pp 41. 

Diaz-Ramos, S., D.L. Stevens, Jr., and A.R. Olsen. 1996. EMAP Statistics Methods 
Manual. EPA/620/R-96/002. Corvallis, OR: U.S. Environmental Protection 
Agency, Office of Research and Development, National Health and Environmental 
Effects Research Laboratory. 

Durning, A.T. 1996. The six floods. WorldWatch November/December 1996. pp. 28-36. 

Geider, R. J. and J. La Roche. 2002. Redfield revisited: variability of C:N:P in marine 
microalgae and its biochemical basis. European Journal Phycology 37: 1-17. 

Holland, A.F. and A.T. Shaughnessey. 1986. Separation of long term variation in benthic 
organisms into major components. In: Oceans 86 Conference Record. Vol. 3. 
Monitoring strategies symposium. Institute of Electrical and Electronic Engineers, 
Piscataway, NJ. pp. 1056-1061. 

Howarth, R.W. J.R. Fruch and D. Sherman. 1991. Inputs of sediment and carbon to an 
estuarine ecosystem: influence of land use. Ecological Applications 1:27-39. 


129 


Hyland, J.L., L. Balthis, C.T. Hackney, G. McRae, A.H. Ringwood, T.R. Snoots, R.F. Van 
Dolah, and T.L. Wade. 1998. Environmental quality of estuaries of the Carolinian 
Province: 1995. Annual statistical summary for the 1995 EMAP- Estuaries 
Demonstration Project in the Carolinian Province. NOAA Technical Memorandum 
NOS ORCA 123 NOAA/NOS, Office of Ocean Resources Conservation and 
Assessment, Silver Spring, MD. 143 p. 

Hyland, J.L., T.J. Herrlinger, T.R. Snoots, A.H. Ring-wood, R.F. Van Dolah, C.T. Hackney, 
G.A. Nelson, J.S. Rosen, and S.A. Kokkinakis. 1996. Environmental Quality of 
Estuaries of the Carolinian Province: 1994. Annual Statistical Summary for the 1994 
EMAP- Estuaries Demonstration Project in the Carolinian Province. NOAA 
Technical Memorandum NOS ORCA 97. NOAA/NOS, Office of Ocean Resources 
Conservation and Assessment, Silver Spring, MD. 102 p. 

Lauenstein, G. G. and A. Y. Cantillo (eds.). 1993. Sampling and analytical methods of the 
National Status and Trends Program National Benthic Surveillance and Mussel 
Watch Projects 1984-1992: Comprehensive descriptions of trace organic analytical 
methods, Volume IV NOAA Technical Memorandum NOS ORCA 71, Silver Spring, 
MD. 182 pp. 

Lauenstein, G.G., Crecelius, E.A. and Cantillo, A.Y. 2000. Baseline metal concentrations 
of the U.S. West Coast and their use in evaluating sediment contamination. 
Presented at 21st Ann. Soc. Environ. Toxicology and Chemistry meeting, 

November 12 - 15, 2000, Nashville Tennessee. 

Lee, H.ll, B. Thompson, and S. Lowe. 2003. Estuarine and scalar patterns of invasion in 
the soft-bottom benthic communities of the San Francisco estuary. Biological 
Invasions 5:85-102. 

Leppakoski, E. 1979. The use of zoobenthos in evaluating effects of pollution in brackish- 
water environments. In: The use of ecological variables in environmental 
monitoring. The National Swedish Environment Protection Board, Report PM 1151. 
pp. 151-157. 

Long, E.R., D.D. MacDonald, S.L. Smith, and F.D. Callander. 1995. Incidence of adverse 
biological effects within ranges of chemical concentrations in marine and estuarine 
sediments. Environmental Management 19:81-97. 

Long, E.R., Hameedi, J., Robertson, A., Dutch, M., Aasen, S., Welch, K., Magoon, S., 

Carr, R., Johnson, T., Biedenbach, J., Scott, K., Mueller, C., and Anderson, J. 2000. 
Sediment Quality in Puget Sound. Year 2 - Central Puget Sound. National Oceanic 
and Atmospheric Administration, National Ocean Service, Silver Spring, MD. NOS 
NCCOS CCMA Technical Memo No. 147 , and Washington State Department of 
Ecology, Olympia, WA, Publication No. 00-03-055. pp. 353. 

Macauley, J.M., J.K. Summers, P.T. Heitmuller, V.D. Engle, G.T. Brooks, M. Babikow, and 
A.M. Adams. 1994. Annual Statistical Summary: EMAP - Estuaries Louisiana 
Province - 1992. U.S. EPA Office of Research and Development, Environmental 
Research Laboratory, Gulf Breeze, FL. EPA/620/R-94/002. 82 p. plus Appendix A. 


130 


Macauley, J.M., J.K. Summers, V.D. Engle, P.T. Heitmuller, and A.M. Adams. 1995. 

Annual Statistical Summary: EMAP - Estuaries Louisiana Province -1993. U.S. EPA 
Office of Research and Development, Environmental Research Laboratory, Gulf 
Breeze, FL. EPA/620/R-96/003. 95 p. 

Reish, D.J. 1986. Benthic invertebrates as indicators of marine pollution: 35 years of 

study. In: Oceans 86 Conference Record. Vol. 3. Monitoring strategies symposium. 
Institute of Electrical and Electronic Engineers, Piscataway, NJ pp. 885-888. 

Simenstad, C.A., J.A. Estes, and K.W. Kenyon. 1978. Aleuts, sea otters, and alternate 
stable state communities. Science 200:403-411 

Simenstad, C.A. and R. Thom. 1995. Spartina alterniflora (smooth cordgrass) as an 

invasive halophyte in Pacific Northwest estuaries. Hortus Northwest 6:9-12, 38-39. 

Stevens, D.L. Jr. 1997. Variable density grid-based sampling designs for continuous 
spatial populations. Environmetrics 8:167-195. 

Stevens, D. I., Jr. and A.R. Olsen. 1999. Spatially restricted surveys over time for 
aquatic resources. J. of Agricultural, Biological and Environmental Statistics: 
4-415-428. 

Strobel, C.J., H.W. Buffum, S.J. Benyi, E.A. Petrocelli, D.R. Reifsteck, and D.J. Keith. 

1995. Statistical summary: EMAP - Estuaries Virginian Province - 1990 to 1993. 

U.S. EPA National Health and Environmental Effects Research Laboratory, Atlantic 
Ecology Division, Narragansett, R.l. EPA/620/R-94/026. 72 p. plus Appendices 
A-C. 

Strobel, C.J., S.J. Benyi, D.J. Keith, H.W. Buffum, and E.A. Petrocelli. 1994. Statistical 
summary: EMAP -Estuaries Virginian Province - 1992. U.S. EPA Office of 
Research and Development, Environmental Research Laboratory, Narragansett, 

Rl. EPA/620/R-94/019. 63 p. plus Appendices A-C. 

Summers, J.K., J.M. Macauley, P.T. Heitmuller, V.D. Engle, A.M. Adams, and G.T. 

Brooks. 1993. Annual Statistical Summary: EMAP-Estuaries Louisianian Province - 
1991. U.S. Environmental Protection Agency, Office of Research and 
Development, Environmental Research Laboratory, Gulf Breeze, FL. EPA/620/R- 
93/007. p. plus Appendices A-C. 

Taylor, J. 1987. Quality assurance of chemical measurements. Lewis Publishers, Inc, 
Chelsea, Ml. 

T N & Associates, Inc. 2001. Compiling Lists of Nonindigenous Species (NIS) from the 
West Coast of the Unites States, Excluding San Francisco Bay. Final Report 
submitted to: National Center for Environmental Assessment - Washington Office, 
U.S. Environmental Protection Agency, Washington, D.C. Contract No. 68-C-98- 
187. 11 p. plus Appendices, plus Spreadsheet. w 

U.S. EPA. 1994a. Methods for Assessing the Toxicity of Sediment-associated 

Contaminants with Estuarine and Marine Amphipods. Office of Research and 
Development, Environmental Monitoring and Systems Laboratory, Cincinnati, OH. 
EPA 600-R-94-025. June 1994. 


131 


U.S. EPA. 1994b. Environmental Monitoring and Assessment Program (EMAP): 
Laboratory Methods Manual - Estuaries, Volume 1: Biological and Physical 
Analyses. Office of Research and Development, Environmental Monitoring and 
Systems Laboratory, Cincinnati, OH. EPA/600/4-91/024. 321-324. 

U.S. EPA. 2000. Clean Water Action Plan: National Coastal Condition Report. United 
States Environmental Protection Agency, Office of Research and Development/ 
Office of Water. Washington D.C. EPA620-R-00-004 

U.S. EPA. 2001a. Environmental Monitoring and Assessment Program (EMAP): National 
Coastal Assessment Quality Assurance Project Plan 2001-2004. United States 
Environmental Protection Agency, Office of Research and Development, National 
Health and Environmental Effects Research Laboratory, Gulf Ecology Division, 

Gulf Breeze, FL. EPA/620/R-01/002. 

U.S. EPA. 2001b. National Coastal Assessment: Field Operations Manual. EPA/620/R- 
01/003. 71 pp. 

U.S. EPA. 2004. National Coastal Condition Report II. EPA/620/R-03/002. In press. 

U.S. General Accounting Office (GAO). 2000. Water Quality - EPA and State Decisions 
Limited by Inconsistent and Incomplete Data. Report to the Chairman, 
Subcommittee on Water Resources and Environment, Committee on 
Transportation and Infrastructure, House of Representatives. Report GAO/RCED 
00-54. 78 pp. 

U.S. Geological Survey (USGS). 2000. Toxicity testing of sediments from the 

BEST/EMAP Western Estuary Group monitoring study. Report Submitted by the 
USGS Columbia Environmental Research Center, Marine Ecotoxicology Research 
Station to the U.S. Geological Survey. Biomonitoring and Environmental Status 
and Trends Program, 6006 Schroeder Road, Madison, Wl, 10 pp. + 22 tables, 3 
figures and 4 attachments. 

U.S. Geological Survey (USGS). 2001. H4IIE bioassay-derived 2,3,7,8 - 

tetrachlorodibenzo-p-dioxin equivalents (TCDD-EQ) in fish collected in 1999 from 
small estuaries along the western coast of the United States. Report Submitted by 
the USGS Columbia Environmental Research Center to the U.S. Geological 
Survey. Biomonitoring and Environmental Status and Trends Program, 6006 
Schroeder Road, Madison, Wl, 16 pp. + 8 figures,10 tables. 

Weisberg, S.B., J.B. Frithsen, A.F. Holland, J.F. Paul, K.J. Scott, J.K. Summers, H.T. 
Wilson, R. Valente, D.G. Heimbuch, J. Gerritsen, S.C. Schimmel, and R.W. 

Latimer. 1992. EMAP- Estuaries Virginian Province 1990 demonstration project 
report. U.S. EPA Environmental Research Laboratory, Narragansett, R.l. 
EPA/600/R-92/100. 


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